@article {pmid40841555,
year = {2025},
author = {Wang, T and Zhang, P and Anantharaman, K and Wang, H and Zhang, H and Zhang, M and Xu, J},
title = {Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7806},
pmid = {40841555},
issn = {2041-1723},
support = {42377469//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001151//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Microbiota/genetics ; Lakes/microbiology/virology ; *Fresh Water/microbiology/virology ; Ecosystem ; Metagenome ; *Viruses/genetics/classification ; *Bacteria/genetics/virology ; Pesticides ; *Host Microbial Interactions/genetics ; Stress, Physiological ; Climate Change ; },
abstract = {Virus-host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.},
}

*Metagenomics/methods
Microbiota/genetics
Lakes/microbiology/virology
*Fresh Water/microbiology/virology
Ecosystem
Metagenome
*Viruses/genetics/classification
*Bacteria/genetics/virology
Pesticides
*Host Microbial Interactions/genetics
Stress, Physiological
Climate Change

@article {pmid40841038,
year = {2025},
author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X},
title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {610-620},
doi = {10.1016/j.jes.2025.02.028},
pmid = {40841038},
issn = {1001-0742},
mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.},
}

Animals
*Manure
*Drug Resistance, Microbial/genetics
*Snails/microbiology
Humans
Introduced Species
Gastrointestinal Microbiome
Soil Microbiology
Environmental Monitoring
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid40841030,
year = {2025},
author = {Nie, E and He, P and Zhang, H and Lü, F},
title = {Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {516-526},
doi = {10.1016/j.jes.2024.10.007},
pmid = {40841030},
issn = {1001-0742},
mesh = {Anaerobiosis ; *Microbiota ; Metagenomics ; *Temperature ; *Metagenome ; Archaea/genetics ; Bacteria/genetics ; },
abstract = {Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion. However, the specific microbial communities and their functions across a wide temperature range still remain elusive. This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35, 44, 53, 55, and 65 °C. A total of 84 metagenome assembled genomes (MAGs) were assembled, with over 65 % of these MAGs corresponding to novel bacterial and archaeal species (including Firmicutes, Chloroflexota, Bacteroidia and Methanobacteriota), greatly enhancing our current comprehension anaerobic digestion process. Notably, functional annotation identified that 44_bin.2 (Methanothrix_A sp. 001602645) harbors enzymes associated with hydrogenotrophic metabolism. Additionally, this microorganism exhibited diverse metabolic capabilities at 44 °C, a temperature commonly employed in industrial practice yet less explored in bench studies. Consequently, it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature, as opposed to the conventional mesophilic range. The microorganism exhibited a variety of metabolic capabilities at 44 °C, a temperature frequently employed in industrial applications but underexplored in laboratory investigations. The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.},
}

Anaerobiosis
*Microbiota
Metagenomics
*Temperature
*Metagenome
Archaea/genetics
Bacteria/genetics

@article {pmid40838847,
year = {2025},
author = {Gao, X and Zheng, Y and Chang, H and Liu, J and Sun, X and Ren, Y and Li, L and Zhao, G and Cheng, Y and Ma, S and Zhao, J and Deng, J and Kang, T and Qiao, Z and Zhao, H and Xie, D and Wang, T and Li, S and Shi, H and Shi, A and Zhang, P},
title = {Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.},
journal = {Journal of medical virology},
volume = {97},
number = {8},
pages = {e70570},
doi = {10.1002/jmv.70570},
pmid = {40838847},
issn = {1096-9071},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Virome ; *Arthritis, Rheumatoid/diagnosis/virology ; *Metagenomics ; Male ; Female ; Middle Aged ; *Palatine Tonsil/virology ; Adult ; *Viruses/genetics/classification/isolation & purification ; Aged ; Microbiota ; },
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease whose exact pathogenesis remains unclear, despite links to genetics, environmental factors, and microbial dysbiosis. Recent studies have highlighted the role of the microbiome in RA, yet the contribution of the tonsil virome remains unexplored. This study aims to investigate whether changes in the tonsil virome are associated with RA progression and assess its diagnostic potential. Using metagenomic data from 32 RA patients and 30 healthy controls (HCs), we identified 45 782 viral operational taxonomic units (vOTUs), with 14 341 classified as core vOTUs. RA patients exhibited significantly reduced virome richness and diversity, whereas Siphoviridae and Microviridae dominated both groups. Statistical analysis identified 235 RA-associated viral markers, including 13 enriched in RA and 222 in HCs. RA-enriched markers were primarily bacteriophages infecting Streptococcaceae, whereas HCs displayed more diverse viral-host interactions. Random forest models demonstrated strong discriminatory power of viral markers in distinguishing RA patients from HCs, achieving an AUC of 0.960, outperforming bacterial markers. Correlation analyses further linked viral markers to immune cell subsets, suggesting that tonsil virome alterations may influence immune dysregulation in RA. This study reveals significant changes in the tonsil virome of RA patients, highlighting its potential as a diagnostic tool and offering new insights into RA pathogenesis. These findings pave the way for future research into the virome's role in autoimmune diseases and therapeutic development.},
}

Humans
*Virome
*Arthritis, Rheumatoid/diagnosis/virology
*Metagenomics
Male
Female
Middle Aged
*Palatine Tonsil/virology
Adult
*Viruses/genetics/classification/isolation & purification
Aged
Microbiota

@article {pmid40836310,
year = {2025},
author = {Wang, X and Dong, Q and Huang, P and Yang, S and Gao, M and Zhang, C and Zhang, C and Deng, Y and Huang, Z and Ma, B and Jiao, Y and Zhou, Y and Wu, T and Zou, H and Shi, J and Sheng, Y and Wang, Y and Consortium, C and Tang, L and Hu, S and Duan, Y and Sun, W and Chen, W and Zhai, Q and Kong, X and Chen, L},
title = {The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {188},
pmid = {40836310},
issn = {2049-2618},
support = {32270077//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Genome, Viral ; Feces/virology/microbiology ; *Genetic Variation ; *Polymorphism, Single Nucleotide ; *Viruses/genetics/classification/isolation & purification ; China ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities.

RESULTS: Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral operational taxonomic units (vOTUs), nearly 90% of which are likely absent from current databases. Analysis of single-nucleotide variations (SNVs) in 233 globally prevalent vOTUs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. Video Abstract CONCLUSIONS: Our analysis underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Virome/genetics
Genome, Viral
Feces/virology/microbiology
*Genetic Variation
*Polymorphism, Single Nucleotide
*Viruses/genetics/classification/isolation & purification
China
Bacteria/genetics/classification
High-Throughput Nucleotide Sequencing

@article {pmid40801952,
year = {2025},
author = {Eckl-Dorna, J and Pjevac, P},
title = {[Principles of microbiome research].},
journal = {HNO},
volume = {73},
number = {9},
pages = {605-609},
pmid = {40801952},
issn = {1433-0458},
mesh = {*Microbiota/genetics ; Humans ; *Metagenomics/methods ; },
abstract = {Microbiome research in the ear nose and throat (ENT) field has substantially gained in importance in recent decades. Modern sequencing methods have largely replaced traditional cultivation. Standardized protocols are essential to ensure reliable and comparable data. The article explains key terms, such as microbiome (the entire microbial community and its environment) and microbiota (only living microorganisms), along with the microbial taxonomy. Important measures for microbiome assessment include the alpha-diversity (species richness and distribution within a sample) and beta-diversity (differences between samples). A differentiation is made between two main approaches to microbiome sequencing: 1) 16S rRNA gene amplicon sequencing (identifies microbial community composition by sequencing the PCR product of a specific gene), 2) metagenomic sequencing (sequences the entire genomic material of a sample, allowing deeper insights). As nasal microbiome biomass is low, careful study design and controls are crucial. Microbiome research is a rapidly growing field with great potential but it requires meticulous planning and bioinformatics expertise for meaningful results.},
}

*Microbiota/genetics
Humans
*Metagenomics/methods

@article {pmid40674970,
year = {2025},
author = {Göçer, S and Arı, O and Göçer, C and Durmaz, R},
title = {Metagenomic analysis of the middle ear microbiome: A next-generation sequencing approach in pediatric patients with and without effusion.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {196},
number = {},
pages = {112487},
doi = {10.1016/j.ijporl.2025.112487},
pmid = {40674970},
issn = {1872-8464},
mesh = {Humans ; Male ; Female ; Child ; Child, Preschool ; *Microbiota/genetics ; *Ear, Middle/microbiology ; *Metagenomics/methods ; *Otitis Media with Effusion/microbiology ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; },
abstract = {OBJECTIVES: Otitis media with effusion (OME) is one of the most common causes of reversible hearing loss in childhood. In recent years, host-microbiota interactions and alterations in microbiota composition associated with health and disease have gained increasing attention in the context of OME. This study aimed to investigate the bacterial microbiota composition of middle ear cavity (MEC) samples obtained from pediatric patients with and without OME. Microbiome differences were analyzed according to clinical groups and variables such as age and gender.

METHODS: 16S rRNA-based metagenomic sequencing was performed on MEC samples (n = 80) and nasopharyngeal samples (n = 20) obtained from 80 children-40 diagnosed with bilateral or unilateral OME (OME group) and 40 undergoing cochlear implant surgery without any history of otitis media (control group). The study cohort included 37 males and 43 females, aged between 2 and 11 years (mean age: 5.2 years).

RESULTS: Sequencing analysis revealed that the phyla Firmicutes and Proteobacteria were dominant in MEC samples. In the OME group, Firmicutes were significantly more abundant, whereas Proteobacteria levels were reduced. At the genus level, Alloiococcus was significantly enriched in the OME group, while genera considered potentially protective, such as Lactobacillus and Propionibacterium, were significantly decreased. Age was not significantly associated with microbial richness or evenness, suggesting stability of microbiota composition across age groups. However, a significantly higher relative abundance of Ralstonia was observed in female patients, suggesting that gender-related hormonal or immunological differences may influence the middle ear microbiota.

CONCLUSION: This study identifies a distinct microbiota profile associated with OME and suggests that host factors, particularly gender, may contribute to shaping the microbial and immunological landscape of the middle ear. These findings also indicate that the microbial environment in OME may shift toward a low-diversity, pathobiont-dominant state.},
}

Humans
Male
Female
Child
Child, Preschool
*Microbiota/genetics
*Ear, Middle/microbiology
*Metagenomics/methods
*Otitis Media with Effusion/microbiology
*High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/genetics
Case-Control Studies

@article {pmid40626910,
year = {2025},
author = {Kust, A and Zorz, J and Paniker, CC and Bouma-Gregson, K and Krishnappa, N and Liu, W and Banfield, JF and Diamond, S},
title = {Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40626910},
issn = {1751-7370},
support = {//Shurl and Kay Curci Foundation/ ; GBMF9321//Gordon and Betty Moore Foundation/ ; },
mesh = {*Cyanobacteria/genetics/classification/physiology ; *Microbiota ; Metagenomics ; *Microbial Consortia ; Fresh Water/microbiology ; Plasmids/genetics ; Metagenome ; },
abstract = {Cyanobacteria are integral to biogeochemical cycles, influence climate processes, and hold promise for commercial applications. In natural habitats, they form complex consortia with other microorganisms, where interspecies interactions shape their ecological roles. Although in vitro studies of these consortia have significantly advanced our understanding, they often lack the biological replication needed for robust statistical analysis of shared microbiome features and functions. Moreover, the microbiomes of many model cyanobacterial strains, which are central to our understanding of cyanobacterial biology, remain poorly characterized. Here, we expanded on existing in vitro approaches by coculturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources, generating 108 stable consortia. Metagenomic analyses revealed that, despite host and inoculum diversity, these consortia converged on a similar set of noncyanobacterial taxa, forming a 25-species core microbiome. The large number of stable consortia in this study enabled statistical validation of both previously observed and newly identified core microbiome functionalities in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis. Furthermore, core species showed significant enrichment of plasmids, and functions encoded on plasmids suggested plasmid-mediated roles in symbiotic interactions. Overall, our findings uncover the potential microbiomes recruited by key model cyanobacteria, demonstrate that laboratory-enriched consortia retain many taxonomic and functional traits observed more broadly in phototroph-heterotroph assemblages, and show that model cyanobacteria can serve as robust hosts for uncovering functional roles underlying cyanobacterial community dynamics.},
}

*Cyanobacteria/genetics/classification/physiology
*Microbiota
Metagenomics
*Microbial Consortia
Fresh Water/microbiology
Plasmids/genetics
Metagenome

@article {pmid40833800,
year = {2025},
author = {Kaspersen, HP and Estensmo, EL and Slettemeås, JS and Haverkamp, THA and Sjurseth, SK and Granstad, S and Sekse, C and Frederiksen, RF and Urdahl, AM},
title = {Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
doi = {10.1099/mgen.0.001466},
pmid = {40833800},
issn = {2057-5858},
mesh = {Animals ; *Monensin/pharmacology ; *Turkeys/microbiology ; *Bifidobacterium/drug effects/genetics/classification/isolation & purification ; Poultry Diseases/prevention & control/microbiology ; Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; Norway ; Female ; Male ; Coccidiosis/veterinary/prevention & control ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; *Coccidiostats/pharmacology ; },
abstract = {Intestinal tissue damage caused by coccidiosis is an important predisposing factor for necrotic enteritis in turkeys, and both diseases are common health issues in turkey production. In Norway, the in-feed ionophore coccidiostat monensin has been used as a preventive measure to combat coccidiosis since the late 1980s. In 2022, however, preventive use of monensin was phased out, which led to an undesired increase in antibiotic treatments among turkey flocks, largely due to necrotic enteritis. The aim of this study was to investigate the overall effects of the preventive monensin use and antibiotic treatment on the turkey caecal microbiota. A total of 102 flock samples from the Norwegian turkey population were included, and metagenomic datasets were generated through shotgun sequencing. All datasets were processed with the Taxprofiler pipeline, followed by diversity, redundancy and differential abundance analyses in R. A significant decrease in alpha and beta diversity was observed for the caecal samples from turkeys exposed to monensin, compared with the non-exposed. An increased abundance of Bifidobacterium spp. was observed in the samples from monensin-exposed turkeys, including Bifidobacterium pullorum, Bifidobacterium longum, Bifidobacterium pseudolongum, Bifidobacterium pseudocatenulatum and Bifidobacterium animalis. Additionally, a decrease in Megamonas and Megasphaera species was detected in these samples. Further, species within the Clostridium genus were higher in abundance among the samples from female turkeys compared with male turkeys. The results indicate that the use of monensin seems to decrease the overall diversity and promote the abundance of Bifidobacterium spp. in the caecum of turkeys, while decreasing the abundance of Megamonas and Megasphaera species. The use of monensin may be beneficial for the gut microbiota due to an increase in favourable Bifidobacterium spp. In contrast, treatment with phenoxymethylpenicillin (penicillin V) early in the turkey life cycle does not seem to cause long-term changes in the caecal microbiota composition. However, further studies are needed to investigate the effects of a decreased abundance of Bifidobacterium spp. and increased gut microbiota diversity in turkeys in the absence of monensin use.},
}

Animals
*Monensin/pharmacology
*Turkeys/microbiology
*Bifidobacterium/drug effects/genetics/classification/isolation & purification
Poultry Diseases/prevention & control/microbiology
Cecum/microbiology
*Gastrointestinal Microbiome/drug effects
Norway
Female
Male
Coccidiosis/veterinary/prevention & control
Metagenomics
Anti-Bacterial Agents/pharmacology
*Coccidiostats/pharmacology

@article {pmid40833454,
year = {2025},
author = {Fong, GY and Chan, KG and Goh, WL and Yap, ML},
title = {Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {134},
pmid = {40833454},
issn = {1572-9699},
support = {IPSR/RMC/UTARRF/2022-C1/Y01//Universiti Tunku Abdul Rahman/ ; },
mesh = {Animals ; *Columbidae/microbiology/virology ; *Feces/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Metagenomics ; Viruses/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification/drug effects ; Metagenome ; Malaysia ; *Microbiota ; Biodiversity ; Phylogeny ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.},
}

Animals
*Columbidae/microbiology/virology
*Feces/microbiology/virology
*Bacteria/genetics/classification/isolation & purification/drug effects
Metagenomics
Viruses/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification/drug effects
Metagenome
Malaysia
*Microbiota
Biodiversity
Phylogeny
*Drug Resistance, Microbial/genetics

@article {pmid40832979,
year = {2025},
author = {Zhou, W and Fan, Y and Zhang, X and Liu, M and Jiang, S and Shang, E and Duan, J},
title = {Amelioration of Guishao Yigong Decoction on Colorectal Cancer Through the Integration of 16S rRNA Sequencing and Fecal Metabolomics.},
journal = {Biomedical chromatography : BMC},
volume = {39},
number = {10},
pages = {e70198},
doi = {10.1002/bmc.70198},
pmid = {40832979},
issn = {1099-0801},
support = {ZDXM-3-9//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; },
mesh = {Animals ; *Colorectal Neoplasms/metabolism/drug therapy/microbiology ; *Feces/chemistry/microbiology ; *Drugs, Chinese Herbal/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; Mice ; Metabolomics/methods ; *Metabolome/drug effects ; Male ; },
abstract = {Guishao Yigong Decoction (GYD), a classical formula, has been used to treat colorectal cancer (CRC) in clinical practices. However, its mechanism is still unclear. Increasing evidence suggests that the gut microbiota may serve as a potential target for treating CRC. Therefore, this study aims to elucidate the amelioration and potential mechanism of GYD on CRC by comprehensively analyzing the metagenome of gut microbiota and fecal metabolome. The results indicated that GYD significantly reduced the number and size of adenomas in the mouse colon, decreased spleen index, alleviated mouse emaciation and rectal bleeding, and protected the colonic barrier. 16S rRNA gene sequencing analysis revealed that GYD could markedly improve the dysbiosis of gut microbiota in CRC mice, increasing the abundance of beneficial bacteria and decreasing the abundance of pathogenic bacteria. Furthermore, the disordered fecal metabolic profiling of CRC mice was notably reversed by GYD. Following GYD administration, metabolites such as thiamine pyrophosphate, 3-methylpentanoic acid, and propanoic acid significantly increased, whereas 2-hydroxy-2-methylpropanoic acid, levodopa, and stearic acid remarkably decreased. Correlation analysis further indicated a close relationship between differential gut microbiota and metabolites. In conclusion, the amelioration of GYD on CRC might involve the regulation of gut microbiota and its metabolism.},
}

Animals
*Colorectal Neoplasms/metabolism/drug therapy/microbiology
*Feces/chemistry/microbiology
*Drugs, Chinese Herbal/pharmacology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/drug effects
Mice
Metabolomics/methods
*Metabolome/drug effects
Male

@article {pmid40832781,
year = {2025},
author = {Tian, Y and Xu, Q and Wu, Z and Wang, H and Hu, X and He, N and Li, H and Liu, B and Zhong, Y and Zhang, H and Wang, M and Xiao, L and Li, S and Zou, Y},
title = {Ameliorating Effect of Bifidobacterium breve CM02-09T on High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease in Mice.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {16},
pages = {e70957},
doi = {10.1096/fj.202501250RR},
pmid = {40832781},
issn = {1530-6860},
support = {32100009//National Natural Science Foundation of China-Guangdong Joint Fund/ ; },
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy ; *Diet, High-Fat/adverse effects ; Male ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Mice ; *Bifidobacterium breve/physiology ; *Gastrointestinal Microbiome ; Liver/metabolism/pathology ; },
abstract = {Evidences have demonstrated that the regulation of gut microbiota by probiotics can be utilized to prevent nonalcoholic fatty liver disease (NAFLD); Bifidobacterium was widely used as a potential therapeutic alternative for metabolic diseases. In this study, the probiotic functions of Bifidobacterium breve CM02-09T and its effects on NAFLD were investigated through genome annotation and high-fat diet (HFD)-induced mouse model. The genome of B. breve CM02-09T consists of a single circular chromosome of 2 372 890 bp. Eighteen male C57BL/6J mice were fed a normal chow diet (NCD), a high-fat diet, and a high-fat diet (HFD) with B. breve CM02-09T separately for 12 weeks. Histopathology, lipid content, biochemical markers in the liver and blood, and metagenomics were assessed and compared. Our results indicate that supplementation with B. breve CM02-09T alleviated liver damage, reduced fat accumulation in the liver and epididymal adipose tissue, decreased TNF-α concentration, and improved NAFLD activity scores. Metagenomic analysis revealed that administration of B. breve CM02-09T promoted a decreased Firmicutes/Bacteroidetes ratio (F/B), an increase in beneficial bacteria, and enhanced lipid metabolism functions. Correlation analysis between the differential species and NAFLD-related indicators suggested that the anti-NAFLD effect of B. breve CM02-09T is related to the gut microbiota. Therefore, B. breve CM02-09T attenuates NAFLD by modulating the gut microbiota and could be used as an alternative therapeutic strategy.},
}

Animals
*Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy
*Diet, High-Fat/adverse effects
Male
*Probiotics/pharmacology
Mice, Inbred C57BL
Mice
*Bifidobacterium breve/physiology
*Gastrointestinal Microbiome
Liver/metabolism/pathology

@article {pmid40795028,
year = {2025},
author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.},
journal = {FEMS microbiology letters},
volume = {372},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf078},
pmid = {40795028},
issn = {1574-6968},
support = {RS-2024-00456300//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; RS-2024-00406488//Ministry of Health and Welfare/ ; },
mesh = {Animals ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Humans ; Republic of Korea ; *Diptera/microbiology ; Phylogeny ; DNA, Bacterial/genetics ; Metagenomics ; },
abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.},
}

Animals
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Humans
Republic of Korea
*Diptera/microbiology
Phylogeny
DNA, Bacterial/genetics
Metagenomics

@article {pmid40785530,
year = {2025},
author = {Liang, J and He, J and Zhao, J and Yang, Y and Xu, W},
title = {Decline in the Relative Abundance of Antibiotic Resistance Genes in Long-Term Fertilized Soil and Its Driving Factors.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {33},
pages = {20710-20718},
doi = {10.1021/acs.jafc.5c03478},
pmid = {40785530},
issn = {1520-5118},
mesh = {Soil Microbiology ; *Fertilizers/analysis ; *Bacteria/genetics/drug effects/isolation & purification/classification/metabolism ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacterial Proteins/genetics/metabolism ; Microbiota ; Metals, Heavy/analysis ; },
abstract = {The changes in antibiotic resistance genes (ARGs) in long-term fertilized soil remain controversial. We aimed to analyze the variation characteristics of ARGs in long-term fertilized soil using metagenomic sequencing. The relative abundance of ARGs did not increase significantly after 7 years of fertilization. However, a clear decline in the relative abundance of ARGs was observed compared to the data from the 4th year. Microbial adaptation strategies in response to changes in the ARG abundance were associated with shifts in microbiome composition and function. Among these, bacterial abundance was the primary driving factor. Additionally, total heavy metal content might serve as the most significant co-selective pressure influencing ARG number. We believe that increasing the selective pressure from heavy metals and antibiotics might result in the loss of certain microbial species and a decrease in ARG abundance. This study provides novel insights into the variations of soil resistance genes under long-term fertilization.},
}

Soil Microbiology
*Fertilizers/analysis
*Bacteria/genetics/drug effects/isolation & purification/classification/metabolism
Soil/chemistry
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*Bacterial Proteins/genetics/metabolism
Microbiota
Metals, Heavy/analysis

@article {pmid40662747,
year = {2025},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {8},
pages = {e0212424},
doi = {10.1128/aem.02124-24},
pmid = {40662747},
issn = {1098-5336},
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Soil/chemistry ; Cities ; Arizona ; *Viruses/genetics/classification/isolation & purification ; Desert Climate ; },
abstract = {Urban green spaces provide essential ecosystem services that are ever more important in arid cities. However, the design and management of these greenspaces often require physicochemical transformations, whose effect in the balance of the arid urban ecosystems is normally not accounted for. In this project, we leverage metagenomic data from soil microbial communities of urban greenspaces and neighboring natural areas in a city from the arid Southwestern USA (Tucson, Arizona) to understand the differences in microbial (bacterial and viral) community structure, taxonomy, and function in urban greenspaces compared to natural arid soils. We found bacterial and viral communities to be distinct between urban greenspace and natural arid soils, with urban greenspace bacteria displaying reduced metabolic versatility and higher genetic potential for simple carbohydrate consumption and nitrogen reduction. Moreover, bacteria in urban greenspaces exhibit higher genetic potential for resistance to heavy metals and certain clinical antibiotics. Our results suggest that the conversion of arid natural land to urban greenspaces determines the soil microbiome structure and functioning, and potentially its ability to adapt to the changing environment.IMPORTANCEUrban green spaces are critical for the sustainability of arid cities. Nevertheless, they require deep soil physicochemical transformations. Soil bacterial and viral communities are responsible for soil functioning and provision of some ecosystem services, but they are also highly influenced by changes in the soil environment. The significance of our research is in illustrating the structural and functional changes that microbial and viral communities undergo in urban soils of arid cities and their potential impacts on urban greenspace soil processes.},
}

*Soil Microbiology
*Bacteria/genetics/classification/isolation & purification
*Microbiota
Soil/chemistry
Cities
Arizona
*Viruses/genetics/classification/isolation & purification
Desert Climate

@article {pmid40478395,
year = {2025},
author = {Zhang, T and Liu, Y and Li, J and Yuan, M and Qiao, C and Huang, X and Yang, X and Gao, B and Lou, C and Yang, Y and Cao, Y},
title = {Toad's survivability and soil microbiome alterations impacted via individual abundance.},
journal = {Biologia futura},
volume = {76},
number = {3},
pages = {399-411},
pmid = {40478395},
issn = {2676-8607},
support = {CI2021A04012//CACMS Innovation Fund/ ; ZZ16-YQ-04//Fundamental Research Funds of CACMS/ ; H2023406026//Hebei Natural Science Foundation/ ; QN2024119//Science Research Project of Hebei Education Department/ ; },
mesh = {Animals ; *Soil Microbiology ; *Microbiota/physiology ; *Bufonidae/microbiology/physiology ; },
abstract = {Artificial breeding is a valid strategy for the reverse of current extinction tendency in wild population of amphibian like toads. Considering public health, an alternative to antibiotics is demanded for ameliorating survival of toads during the culture period. Relying on the cognition of probiotics or antagonistic bacteria, the present work investigated viability and soil microorganism variations induced by distribution characteristic on toads using high-throughput sequencing technology. Comparison and analysis of soil metagenome from clustered and depopulated groups distinguished by toad behavior showed differences of bacterial community composition (e.g., Proteobacteria bacterium TMED72 and Nannocystis exedens) and antibiotic resistance genes involving antibiotic efflux and inactivation (e.g., mdtB and acrF). There were 18 and 10 distribution-typical genes independently enriched in Proteobacteria bacterium TMED72 and bacterium TMED88 of clustered group and Nannocystis exedens of depopulated group. In Nannocystis exedens, one of the distribution-typical genes was annotated as 6-phosphogluconate dehydrogenase acting role on bacterial growth restriction. It implied that, compared with the group emerging rare traces, the reduction of soil bacteria which possess genes retarding bacterial growth putatively impairs competitiveness to pathogenic bacteria and results in poor survivability of toads under clustering behavior. With the co-occurrence of virulence genes, more evidences are needed on the antagonistic bacteria Nannocystis exedens as antibiotic substitute.},
}

Animals
*Soil Microbiology
*Microbiota/physiology
*Bufonidae/microbiology/physiology

@article {pmid40325330,
year = {2025},
author = {Panicucci, C and Casalini, S and Fiorito, G and Rinaldi, AB and Biagioli, V and Cangelosi, D and Brolatti, N and Principi, E and Baratto, S and Pedemonte, M and Morando, S and Riva, A and Venturino, C and Striano, P and Uva, P and Bruno, C},
title = {Exploratory Analysis of Gut Microbiota Profile in Duchenne Muscular Dystrophy (DMD) Patients with Intellectual Disability.},
journal = {Molecular neurobiology},
volume = {62},
number = {9},
pages = {11799-11809},
pmid = {40325330},
issn = {1559-1182},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Intellectual Disability/microbiology/complications ; *Muscular Dystrophy, Duchenne/microbiology/complications ; Adolescent ; Male ; Child ; Female ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {This study investigates the differences in gut microbiota composition between DMD patients with (DMD +) and without (DMD -) intellectual disability (ID) and its potential role in cognitive outcomes. In this study, we assessed the gut microbiota in 50 genetically confirmed DMD patients (median age 13.1 years) using 16S rRNA gene sequencing. Cognitive assessment was performed using the Wechsler Intelligence Scales, with ID defined as an IQ < 70. Stool samples were analyzed, and statistical methods were used to assess alpha- and beta-diversity. Thirty-four percent of patients had ID. No significant differences were found in alpha-diversity or in the Firmicutes/Bacteroidetes ratio. However, beta-diversity analysis revealed significant differences between DMD + and DMD - groups, including, in DMD + , an increased abundance of Propionibacterium and Bifidobacterium, and a reduction in Bulleidia. These bacteria are involved in metabolic pathways that can influence neurological health through the gut-brain axis, particularly via the production of short-chain fatty acids. While these preliminary findings suggest a possible association between gut microbiota profile and cognitive impairment in DMD, further research is needed to explore a causal relationship and consider microbiota-targeted therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
*Intellectual Disability/microbiology/complications
*Muscular Dystrophy, Duchenne/microbiology/complications
Adolescent
Male
Child
Female
RNA, Ribosomal, 16S/genetics
Bacteria/genetics

@article {pmid40254787,
year = {2025},
author = {Dame-Teixeira, N and Lynch, J and Yu, X and Cena, JA and Do, T},
title = {The Caries and Caries-Free Archaeome.},
journal = {Journal of dental research},
volume = {104},
number = {10},
pages = {1138-1146},
doi = {10.1177/00220345251329343},
pmid = {40254787},
issn = {1544-0591},
mesh = {*Dental Caries/microbiology ; Humans ; *Archaea/genetics/isolation & purification/classification ; *Dental Plaque/microbiology ; *Saliva/microbiology ; Metagenomics ; Microbiota ; },
abstract = {The difficulty of establishing a relationship between archaea and oral diseases such as dental caries stems from the challenges of detecting, identifying, and isolating these microorganisms. This study aimed to detect archaea in publicly available datasets comprising caries and caries-free saliva and dental plaque by using a tailored bioinformatic pipeline for shotgun sequencing analysis. A systematic search was performed to identify studies using shotgun metagenomics or metatranscriptomics on samples obtained from individuals with dental caries. Two reviewers selected studies based on eligibility criteria. Sequencing and metadata from each study were retrieved from the SRA Bioproject. A count table was generated for each database by mapping reads against an archaea genome database, specifically tailored for this study, using stringent filtering parameters of greater than 97% similarity and 90% query coverage. Archaeal prevalence was determined using an arbitrary cutoff point (>500 reads). An effect size meta-analysis was performed to determine the overall prevalence. Phyloseq and DESeq2 packages were used to determine alpha and beta diversities, differential abundance in different taxonomic levels, and differential expression comparing caries and caries-free samples. Spearman correlation was performed with the bacteriome. The search yielded 154 titles, from which a collection of 7 datasets from 8 studies was obtained. Of 397 samples, N = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%-40%) and identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria. Methanogens were present in both the caries and caries-free groups (Methanobrevibacter spp., Methanosarcina, and Methanosphaera) and positively correlated with Stenotrophomonas, Streptococcus, Actinomyces, Abiotrophia, Gemella, and Corynebacterium. Several methanogenesis genes, including methyl-coenzyme M reductase, which catalyzes the final step of methane production in methanogens, were underexpressed in caries-active samples compared with caries-free samples. Saliva and dental plaque emerged as sites of low-abundance archaea, with methanogenesis genes underexpressed in caries-active samples.},
}

*Dental Caries/microbiology
Humans
*Archaea/genetics/isolation & purification/classification
*Dental Plaque/microbiology
*Saliva/microbiology
Metagenomics
Microbiota

@article {pmid40830497,
year = {2025},
author = {Marialva, EF and Martins-Campos, KM and de Almeida, VR and Ríos-Velasquez, CM and Tempone, AJ and Pessoa, FAC and Traub-Cseko, YM},
title = {Investigation of bacterial microbiota variability in two allopatric populations of Nyssomyia umbratilis, susceptible and nonsusceptible to Leishmania (Viannia) guyanensis infection in the Amazon region.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {354},
pmid = {40830497},
issn = {1756-3305},
mesh = {Animals ; *Psychodidae/microbiology/parasitology ; Brazil ; Female ; *Leishmania guyanensis/physiology ; *Insect Vectors/microbiology/parasitology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Humans ; },
abstract = {BACKGROUND: Sand flies of the species Nyssomyia umbratilis (Diptera: Psychodidae: Phlebotominae) are vectors of the parasite Leishmania (Viannia) guyanensis, one of the etiological agents of cutaneous leishmaniasis in the Amazon region. In addition, Ny. umbratilis is a cryptic species, with populations showing differences in their ability to transmit the parasite. For instance, populations of Ny. umbratilis from the Manacapuru municipality (MAN), located on the south bank of the Negro river, in the Amazonas state of Brazil, shows refractoriness to Leishmania infection, while populations from Rio Preto da Eva municipality (RPE), located on the north bank of the Negro river, are susceptible to infection. This lack of vectorial capacity may be caused by several factors, including the intestinal bacterial microbiota of sand flies.

METHODS: In this work, we carried out a metagenomic study of the intestinal microbiota of Ny. umbratilis populations from MAN and RPE. Ny. umbratilis females were collected in forested areas, sand fly midguts were dissected, DNA was extracted, and the 16 S rRNA gene sequenced to identify the bacterial composition of the microbiota.

RESULTS: In total, 16 phyla, 33 classes, 49 orders, 93 families, and 112 genera of bacteria were identified. The phylum Proteobacteria was the most frequent (85.9%) in both localities, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes with, 9.9%, 4.9%, and 4.4%, respectively. In MAN, 84 genera were identified and 79 in RPE, with MAN having a greater richness compared with RPE. Among these, the genera Rickettsia, Prevotella, Porphyromonas, Peptostreptococcus, and Caulobacter were the most prevalent in MAN, and the genera Rickettsia, Prevotella, Cryocola, Porphyromonas, and Caulobacter were the most prevalent in RPE.

CONCLUSIONS: Bacterial microbiota from MAN insects presents a greater diversity in relation to the RPE insects. Some of the identified bacteria have the potential to be used in alternative transmission control approaches as the development of transgenic vectors, and also, bacteria found exclusively in MAN sand flies may be candidates for a future transmission control approach to combat leishmaniasis in the Amazon region.},
}

Animals
*Psychodidae/microbiology/parasitology
Brazil
Female
*Leishmania guyanensis/physiology
*Insect Vectors/microbiology/parasitology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Microbiota
Humans

@article {pmid40829558,
year = {2025},
author = {Huang, WC and Spang, A},
title = {DPANN archaea.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R791-R794},
doi = {10.1016/j.cub.2025.06.038},
pmid = {40829558},
issn = {1879-0445},
mesh = {*Archaea/genetics/physiology/classification/metabolism ; *Symbiosis ; Phylogeny ; *Genome, Archaeal ; Biological Evolution ; },
abstract = {Archaea are one of the two primary domains of life alongside Bacteria. Extant archaea play an important role in global nutrient cycles and comprise members that were crucial for the evolution of life on Earth including the origin of eukaryotic cells through a symbiotic integration of an archaeal and bacterial partner. Despite their importance in ecology and evolution, our knowledge of archaeal diversity and function remains limited in part because it has proven challenging to cultivate archaea in the laboratory. Over the last two decades, the use of novel cultivation-independent approaches such as metagenomics has not only led to the discovery of a vast diversity of previously unknown archaeal lineages but also provided a window into their genomic content, allowing researchers to make predictions about metabolic functions and lifestyles. For example, by combining genomics approaches with phylogenetic analyses (that is, the reconstruction of species trees) researchers have uncovered several phylum-level lineages of putative genome-reduced archaea referred to as the 'DPANN' archaea, whose members were shown to have limited metabolic capabilities, indicating their dependency on symbiotic partners. These findings are consistent with observations from cultivation-based studies that have succeeded in enriching some of these small-cell symbionts in co-cultures with their hosts. Although they were initially discovered in extreme environments, DPANN archaea have now been shown to be widespread across a variety of environments and may thus play an important role in not only host evolution but also ecology. Herein, we aim to highlight DPANN archaea by providing an overview of their diversity, genomic and metabolic features, unique cell biology and interactions, and evolutionary origins. We also underscore several fascinating topics that remain underexplored.},
}

*Archaea/genetics/physiology/classification/metabolism
*Symbiosis
Phylogeny
*Genome, Archaeal
Biological Evolution

@article {pmid40254701,
year = {2025},
author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K},
title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40254701},
issn = {1867-1314},
abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.},
}

@article {pmid39966546,
year = {2025},
author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and Mihula, M and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M},
title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.},
journal = {Pediatric research},
volume = {97},
number = {7},
pages = {2267-2271},
pmid = {39966546},
issn = {1530-0447},
mesh = {Humans ; Female ; *Milk, Human/immunology/chemistry ; Pregnancy ; Infant, Newborn ; *Anti-Bacterial Agents/adverse effects ; *Immunoglobulin A/metabolism ; Case-Control Studies ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Translational Research, Biomedical ; *Microbiota/drug effects ; Adult ; *Prenatal Exposure Delayed Effects ; },
abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.

METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N = 41 + 41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.

RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.

CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.

IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.},
}

Humans
Female
*Milk, Human/immunology/chemistry
Pregnancy
Infant, Newborn
*Anti-Bacterial Agents/adverse effects
*Immunoglobulin A/metabolism
Case-Control Studies
Feces/microbiology/chemistry
*Gastrointestinal Microbiome/drug effects
Translational Research, Biomedical
*Microbiota/drug effects
Adult
*Prenatal Exposure Delayed Effects

@article {pmid32564244,
year = {2020},
author = {Mokkala, K and Houttu, N and Koivuniemi, E and Sørensen, N and Nielsen, HB and Laitinen, K},
title = {GlycA, a novel marker for low grade inflammation, reflects gut microbiome diversity and is more accurate than high sensitive CRP in reflecting metabolomic profile.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {16},
number = {7},
pages = {76},
pmid = {32564244},
issn = {1573-3890},
mesh = {Acetylglucosamine/blood ; Adult ; Biomarkers/blood ; C-Reactive Protein/metabolism ; Cardiovascular Diseases/blood/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; Female ; Fibrinogen/metabolism ; Gastrointestinal Microbiome/*physiology ; Glycoproteins/blood ; Haptoglobins/metabolism ; Humans ; Inflammation/blood/*metabolism ; Metabolomics/methods ; Obesity/blood/metabolism ; Pregnancy ; Serum Amyloid A Protein/metabolism ; },
abstract = {INTRODUCTION: Gut microbiota is, along with adipose tissue, recognized as a source for many metabolic and inflammatory disturbances that may contribute to the individual's state of health.

OBJECTIVES: We investigated in cross-sectional setting the feasibility of utilizing GlycA, a novel low grade inflammatory marker, and traditional low grade inflammatory marker, high sensitivity CRP (hsCRP), in reflecting serum metabolomics status and gut microbiome diversity.

METHODS: Fasting serum samples of overweight/obese pregnant women (n = 335, gestational weeks: mean 13.8) were analysed for hsCRP by immunoassay, GlycA and metabolomics status by NMR metabolomics and faecal samples for gut microbiome diversity by metagenomics. The benefits of GlycA as a metabolic marker were investigated against hsCRP.

RESULTS: The GlycA concentration correlated with more of the metabolomics markers (144 out of 157), than hsCRP (55 out of 157) (FDR < 0.05). The results remained essentially the same when potential confounding factors known to associate with GlycA and hsCRP levels were taken into account (P < 0.05). This was attributable to the detected correlations between GlycA and the constituents and concentrations of several sized VLDL-particles and branched chain amino acids, which were statistically non-significant with regard to hsCRP. GlycA, but not hsCRP, correlated inversely with gut microbiome diversity.

CONCLUSION: GlycA is a superior marker than hsCRP in assessing the metabolomic profile and gut microbiome diversity. It is proposed that GlycA may act as a novel marker that reflects both the gut microbiome and adipose tissue originated metabolic aberrations; this proposal will need to be verified with regard to clinical outcomes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, NCT01922791, August 14, 2013.},
}

Acetylglucosamine/blood
Adult
Biomarkers/blood
C-Reactive Protein/metabolism
Cardiovascular Diseases/blood/metabolism
Cross-Sectional Studies
Feces/chemistry
Female
Fibrinogen/metabolism
Gastrointestinal Microbiome/*physiology
Glycoproteins/blood
Haptoglobins/metabolism
Humans
Inflammation/blood/*metabolism
Metabolomics/methods
Obesity/blood/metabolism
Pregnancy
Serum Amyloid A Protein/metabolism

@article {pmid40825816,
year = {2025},
author = {Kaushal, M and Kolombia, YA and Alakonya, AE and Masso, C},
title = {Comparing soil microbial diversity in smallholder plantain backyard gardens and main farms in Western and Central Africa.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30220},
pmid = {40825816},
issn = {2045-2322},
support = {HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; },
abstract = {In sub-Saharan Africa (SSA), plantains (Musa spp.) are a staple crop and a vital source of income for smallholder farmers. Despite their importance, the microbial diversity of soils in plantain-growing agroecologies remains poorly understood-particularly how it may influence plant performance and resilience through soil-plant interactions. In this study, we used Illumina MiSeq-based 16S rDNA sequencing to characterize bacterial communities in the rhizosphere of plantains cultivated under two distinct agroecological settings: Backyard gardens and main farms. Analyses of alpha and beta diversity (Sobs, Chao1, ACE, Shannon-Wiener, and Simpson indices; P < 0.05) revealed significant differences in species richness and community structure between the two agroecologies. Actinobacteria (55%) emerged as the dominant phylum, followed by Proteobacteria (21%) and Acidobacteria (15%). Beneficial genera such as Bacillus, Streptomyces, Bradyrhizobium, and Paenibacillus were also detected. Functional predictions based on COG and KEGG databases indicated notable differences in microbial functional potential between the two settings. These results suggest that agroecological context and habitat type strongly influence rhizosphere microbial diversity, with important implications for enhancing plant-microbe interactions and supporting crop resilience in SSA's resource-limited smallholder systems.},
}

@article {pmid40817036,
year = {2025},
author = {Chen, Y and Huang, S and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W},
title = {Viral metagenomics reveals parvovirus dark matter of herbivorous wildlife from the Qinghai-Tibet Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {508},
pmid = {40817036},
issn = {1471-2180},
support = {82341106//National Natural Science Foundation of China/ ; 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; },
abstract = {BACKGROUND: As one of the birthplaces of modern biodiversity, the Qinghai-Tibet Plateau is home to a rich variety of unique animal groups. Herbivorous wildlife constitutes a vital component of the plateau's ecosystems, yet current research on parvoviruses in these species remains limited. With the development of viral metagenomics and next-generation sequencing technology, more and more novel viruses have been detected.

RESULTS: In this study, we collected 741 fecal samples from herbivorous wildlife across three distinct habitats on the Qinghai-Tibet Plateau and employed metagenomics analysis technology to characterize the parvovirus dark matter. We identified 32 parvoviruses by analysis, of which 13 were closely related to the members of Bocapavovirus, Dependoparvovirus and Protoparvovirus in the subfamily of Parvovirinae, 5 belonging to the Densovirinae subfamily, and 5 were classified into the newly proposed subfamily of Hamaparvovirinae. Additionally, 9 parvoviruses remain unclassified and cannot be assigned to any existing subfamily. We conducted a phylogenetic analysis based on the non-structural proteins of the viruses to explore the evolutionary relationships among parvoviruses, and found that some viruses could not be clustered with known parvoviruses.

CONCLUSIONS: These results enrich our understanding of parvovirus and viral dark matter, and reveal that these wild animals carry a large number of unknown new viruses that may have implications for the ecological balance of the Qinghai-Tibet Plateau.},
}

@article {pmid40796349,
year = {2025},
author = {Huang, WC and Probst, M and Hua, ZS and Szánthó, LL and Szöllősi, GJ and Ettema, TJG and Rinke, C and Williams, TA and Spang, A},
title = {Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the Njordarchaeia.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf201},
pmid = {40796349},
issn = {1537-1719},
abstract = {The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focused on characterising the diversity of Asgard archaea in an effort to identify the closest extant relatives of eukaryotes. However, resolving archaeal phylogeny is challenging, and the positions of two recently-described lineages - Njordarchaeales and Panguiarchaeales - are uncertain, in ways that directly bear on hypotheses of early evolution. In initial phylogenetic analyses, these lineages branched either with Asgards or with the distantly-related Korarchaeota, and it has been suggested that their genomes may be affected by metagenomic contamination. Resolving this debate is important because these clades include genome-reduced lineages that may help inform our understanding of the evolution of symbiosis within Asgard archaea. Here, we performed phylogenetic analyses revealing that the Njordarchaeales and Pangiuarchaeales constitute the new class Njordarchaeia within Asgard archaea. We found no evidence of metagenomic contamination affecting phylogenetic analyses. Njordarchaeia exhibit hallmarks of adaptations to (hyper-)thermophilic lifestyles, including biased sequence compositions that can induce phylogenetic artifacts unless adequately modelled. Panguiarchaeum is metabolically distinct from its relatives, with reduced metabolic potential and various auxotrophies. Phylogenetic reconciliation recovers a complex common ancestor of Asgard archaea that encoded the Wood-Ljungdahl pathway. The subsequent loss of this pathway during the reductive evolution of Panguiarchaeum may have been associated with the switch to a symbiotic lifestyle potentially based on H2-syntrophy. Thus, Panguiarchaeum may contain the first obligate symbionts within Asgard archaea.},
}

@article {pmid40795932,
year = {2025},
author = {Teng, ZJ and Yuan, XJ and Liu, R and Xu, SC and Chen, XL and Chen, Y and Zhang, YZ},
title = {Inositol phosphates as an overlooked phosphorous source in marine ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf161},
pmid = {40795932},
issn = {1751-7370},
abstract = {Inositol phosphates, common phosphorus storage compounds that are also crucial for eukaryotic cell signaling, constitute a significant portion of dissolved organic phosphorus in coastal waters. The hydrolysis of inositol phosphates could be an important contributor to phosphorus cycling in phosphorus-limited marine ecosystems, yet this process remains poorly understood in marine contexts. In this study, we reveal substantial concentrations of Inositol phosphates in marine macrophytes, including green, brown, and red algae as well as common seagrasses, suggesting that these organisms are likely major biological sources of inositol phosphates in the oceans. A comprehensive analysis of genes involved in inositol phosphates hydrolysis in global marine metagenomes and metatranscriptomes identified key roles for γ-, α-, and δ-proteobacteria, with additional contributions from Flavobacteriia. The degradation of marine inositol phosphates was predominantly mediated by alkaline β-propeller phytases, though genes associated with acidic cysteine phytases and purple acid phytases were also widely present. Community structure and functional traits linked to inositol phosphates degradation were shaped largely by stochastic processes. Further examination of enzyme activity at the protein and community levels indicated that phytate metabolism by marine microbes is likely a widespread phenomenon in the ocean. Overall, this study highlights inositol phosphates hydrolysis as an essential yet overlooked adaptation by marine microorganisms to address phosphorus limitations in ocean ecosystems.},
}

@article {pmid40795730,
year = {2025},
author = {D'Ugo, E and Mukherjee, A and Resitano, M and Giuseppetti, R and Fortini, D and Bruna Matturro, and Chirico, M and Pisanu, ME and Tucci, M and Pozzi, R and Lovecchio, N and Slawomir, O and Iosi, F and Villa, L and Iorio, E and Aulenta, F and Viggi, CC and Bertuccini, L and Magurano, F},
title = {Fishing out microorganisms for bioremediation using metagenomics: Isolation and whole-genome sequencing of the metabolically versatile Rhodococcus erythropolis LP27217 strain from oil spill lake.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139463},
doi = {10.1016/j.jhazmat.2025.139463},
pmid = {40795730},
issn = {1873-3336},
abstract = {Isolating microorganisms from oil spill-contaminated environments is essential for advancing bioremediation strategies and discovering novel bioprocesses for hydrocarbon degradation. In this study, we report the isolation of a novel strain, Rhodococcus erythropolis LP27217, from Pertusillo Lake (Italy) on february 2017. Water samples were collected during an oil spill event and microbial community was previously characterized using 16S rRNA gene-targeted metagenomic analysis and functional prediction. The Rhodococcus genus was identified as the dominant member of this microbiome, and functional predictive analyses guided the isolation of the R. erythropolis LP27217 strain under various growth conditions, including the presence of hydrocarbons and in Liquid Microbial Fuel Cell (L-MFC) systems. This strain exhibits a versatile hydrocarbon-degrading and transforming metabolism, effectively addressing pollutants such as crude oil, polycyclic aromatic hydrocarbons (PAHs), and dibenzothiophene (DBT), even under psychrophilic conditions. Additionally, R. erythropolis LP27217 demonstrated the ability to produce lipopeptide biosurfactants and lipophilic polymers, with the latter being associated with the formation of an electrogenic hydrocarbonoclastic biofilm at the anoxic oil-water interface. Overall, this study demonstrated that R. erythropolis LP27217 is a promising candidate for sustainable applications, including in situ bioremediation of oil spills in lake ecosystems and the biosynthesis of innovative polymers and biosurfactants for biotechnological and environmental purposes. Furthermore, its ability to operate across oxic and hypoxic conditions, at the oil-water interface and within the water column, highlights a novel microbial mechanism with significant ecological and industrial potential.},
}

@article {pmid40794955,
year = {2025},
author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D},
title = {Decoding longitudinal microbiome trajectories: an interpretable machine learning approach for biomarker discovery and prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40794955},
issn = {1477-4054},
support = {R03 DE034507/DE/NIDCR NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; U01DE025046/NH/NIH HHS/United States ; 1R03DE034507-01/NH/NIH HHS/United States ; },
mesh = {Humans ; *Machine Learning ; *Biomarkers ; *Microbiota ; Longitudinal Studies ; Gastrointestinal Microbiome ; },
abstract = {Information generated from longitudinally sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g. metagenomics) poses analytical challenges.To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g. XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa, but also offers improved prediction accuracy compared with existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. Moreover, LP-Micro highlights critical time points and associated microbial changes: oral microbial changes, including Streptococcus mutans, are most informative for predicting childhood dental disease at around 39 months of age, while gut microbial changes shortly after bariatric surgery strongly predict future weight loss. These findings are both informative and aligned with clinical expectations. The tool LP-Micro can be seen at https://github.com/IV012/LPMicro.},
}

Humans
*Machine Learning
*Biomarkers
*Microbiota
Longitudinal Studies
Gastrointestinal Microbiome

@article {pmid40794299,
year = {2025},
author = {El-Halim, HMA and El-Hadidi, M and Fouad, N and Hamed, RR and Megid, IA and Taha, MH and Radwan, KH},
title = {Metagenomic insight into drought-induced changes in the Egyptian wheat rhizosphere microbiome.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {310},
pmid = {40794299},
issn = {1573-0972},
mesh = {*Triticum/microbiology ; *Rhizosphere ; *Droughts ; Egypt ; *Microbiota/genetics ; Soil Microbiology ; Phylogeny ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Stress, Physiological ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {Wheat is one of the most important cereal crops and an important source of food for billions of people worldwide. However, drought stress can pose a real threat to its productivity and lead to significant yield losses, especially in Egypt. The rhizospheric microbiome of wheat can play an important role in drought stress and help wheat to respond to this abiotic stress. Understanding this microbiome is therefore also important to improve drought stress resilience and productivity. In this study, a metagenomic analysis was performed to investigate how the composition and diversity of microbial communities associated with the wheat rhizosphere change under drought. Taxonomic and phylogenetic analyses revealed a shift in microbial abundance, with Actinobacteria, Bacteroidetes, Proteobacteria and Verrucomicrobia being the four most abundant phyla of the ethnic microbiota. Remarkably, other classes, including Alphaproteobacteria and Cytophagia, were significantly enriched under drought, which could be a promising enhancement of plant stress altruism. Differential abundance analysis showed that the control samples had higher abundance of microbial taxa such as OD1, WS2, Chlorobi, ABY1 and SHA-109 compared to the drought-treated genotypes. Functional prediction analysis using PICRUSt showed that an uncharacterized ATP-binding protein within the AAA + superfamily is overrepresented under drought conditions. This suggests that these genes may play a role in stress adaptation, possibly via energy-dependent regulation of cellular processes involved in plant survival. Our results expand our understanding of the complexity of responses of the wheat rhizosphere microbiome to drought and have practical implications for the development of microbial target combinations to improve wheat tolerance and productivity in the context of climate change challenges.},
}

*Triticum/microbiology
*Rhizosphere
*Droughts
Egypt
*Microbiota/genetics
Soil Microbiology
Phylogeny
*Metagenomics
*Bacteria/classification/genetics/isolation & purification
Stress, Physiological
RNA, Ribosomal, 16S/genetics
Metagenome

@article {pmid40792105,
year = {2025},
author = {Han, W and Zhou, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591076},
pmid = {40792105},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics/methods ; *Feces/microbiology ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy ; *Lung Neoplasms/immunology/microbiology/therapy/drug therapy ; Immunotherapy ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/genetics/drug effects ; },
abstract = {BACKGROUND: Substantial interstudy heterogeneity in cancer immunotherapy-associated biomarkers has hindered their clinical applicability. To address this challenge, we performed a comprehensive integration of publicly available global metagenomic datasets. By leveraging metagenomic profiling and machine learning approaches, this study aimed to elucidate gut microbial signatures associated with immune response in lung cancer (LC) and to evaluate the modulatory effects of antibiotic exposure.

METHODS: A systematic literature search was conducted to identify relevant datasets, resulting in the inclusion of 209 fecal metagenomic samples: 154 baseline samples (45 responders, 37 non-responders, and 72 healthy controls) and 55 longitudinal samples collected during immunotherapy. We performed taxonomic and functional characterization of gut microbiota (GM) differentiating responders from non-responders, delineated microbiome dynamics during treatment, and assessed the impact of antibiotics on key microbial taxa. Among eight machine learning algorithms evaluated, the optimal model was selected to construct a predictive framework for immunotherapy response.

RESULTS: Microbial α-diversity was significantly elevated in responders compared to non-responders, with antibiotic administration further amplifying this difference-most notably at the species level. Integrative multi-omics analysis identified two pivotal microbial biomarkers, s_Bacteroides caccae and s_Prevotella copri, which were strongly associated with immunotherapy efficacy. A random forest-based classifier achieved robust predictive performance, with area under the curve (AUC) values of 0.82 and 0.79 at the species and genus levels, respectively. Notably, P. copri was further enriched in responders with poor progression-free survival (PFS <3 months), indicating a potential deleterious role. Antibiotic exposure significantly influenced the abundance and functional potential of these key taxa. KEGG-based functional analysis revealed the enrichment of amino acid metabolism pathways in responders. Additionally, CARD database annotation demonstrated that the majority of antibiotic resistance genes were associated with Bacteroidetes and Proteobacteria, implicating these taxa in shaping microbial-mediated therapeutic responses.

CONCLUSIONS: This study represents the first large-scale, cross-cohort integration of metagenomic data to identify reproducible GM signatures predictive of immune checkpoint inhibitor efficacy in LC. The findings not only underscore the prognostic relevance of specific taxa but also establish a foundation for developing microbiome-informed, personalized immunotherapeutic strategies.},
}

Humans
*Machine Learning
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
Metagenomics/methods
*Feces/microbiology
*Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy
*Lung Neoplasms/immunology/microbiology/therapy/drug therapy
Immunotherapy
Male
Female
Middle Aged
Aged
Bacteria/classification/genetics/drug effects

@article {pmid40790223,
year = {2025},
author = {Ren, Y and Zhang, P and Yu, H and Li, S and Jiang, H},
title = {Metagenome-based characterization of the gut virome in patients with schizophrenia.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {895},
pmid = {40790223},
issn = {1479-5876},
support = {82170755//National Natural Science Foundation of China/ ; LHYYKYQD20240307//Scientif Research Foudation of People's Hospital of Longhua of Shenzhen/ ; },
mesh = {Humans ; *Schizophrenia/virology/microbiology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; *Metagenome/genetics ; Female ; Adult ; Feces/virology/microbiology ; Middle Aged ; Case-Control Studies ; },
abstract = {BACKGROUND: Schizophrenia (SCZ) is a multifactorial psychiatric disorder increasingly linked to gut microbial dysbiosis. While bacterial alterations have been widely studied, the role of the gut virome in SCZ remains largely unexplored. This study aimed to characterize the gut virome in SCZ and identify potential viral biomarkers associated with the disease.

METHODS: We analyzed fecal metagenomic data from 171 individuals (90 SCZ patients and 81 controls) using the Chinese Gut Virus Catalog (cnGVC). We assessed gut virome diversity, identified SCZ-associated vOTUs, explored virus-bacteria correlations, and evaluated diagnostic potential using random forest models. In addition, we examined follow-up samples from SCZ patients to assess the impact of antipsychotic treatment on the gut virome.

RESULTS: We identified 171 vOTUs that differed significantly between SCZ patients and controls, with 124 enriched in SCZ-mainly from Siphoviridae and Flandersviridae. Correlation analysis revealed altered virus-bacteria interactions in SCZ, including disease-specific associations with Akkermansia and Clostridia. A random forest classifier based on virome features achieved an AUC of 93.2%, outperforming the bacterial model. External validation using ASD and PD cohorts yielded lower AUCs (61.2-67.0%), suggesting disease specificity. In follow-up samples collected after three months of treatment, we observed partial changes in alpha diversity, while beta diversity remained stable, indicating that antipsychotic therapy may alter specific viral taxa without broadly reshaping the overall gut virome structure.

CONCLUSIONS: This study provides evidence of distinct gut virome alterations in SCZ and identifies specific viral markers with strong diagnostic potential. These findings highlight the underappreciated role of the gut virome in psychiatric disorders and support its utility as a non-invasive biomarker for SCZ diagnosis and future therapeutic development.},
}

Humans
*Schizophrenia/virology/microbiology
*Virome/genetics
*Gastrointestinal Microbiome/genetics
Male
*Metagenome/genetics
Female
Adult
Feces/virology/microbiology
Middle Aged
Case-Control Studies

@article {pmid40790024,
year = {2025},
author = {Kiguchi, Y and Hamamoto, N and Kashima, Y and Runtuwene, LR and Ishizaka, A and Kuze, Y and Enokida, T and Tanaka, N and Tahara, M and Kageyama, SI and Fujisawa, T and Yamashita, R and Kanai, A and Tuda, JSB and Mizutani, T and Suzuki, Y},
title = {Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7397},
pmid = {40790024},
issn = {2041-1723},
support = {22fk0108538s0201//Japan Agency for Medical Research and Development (AMED)/ ; },
mesh = {Humans ; Saliva/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; *Mouth/microbiology ; Female ; Male ; Colorectal Neoplasms/microbiology ; Head and Neck Neoplasms/microbiology ; Metagenome ; Adult ; DNA, Bacterial/genetics ; *Bacteria/genetics ; Middle Aged ; Streptococcus/genetics ; },
abstract = {Survival strategy of bacteria is expanded by extrachromosomal elements (ECEs). However, their genetic diversity and functional roles for adaptability are largely unknown. Here, we discover a novel family of intracellular ECEs using 56 saliva samples by developing an efficient microbial DNA extraction method coupled with long-read metagenomics assembly. Even though this ECE family was not hitherto identified, our global prevalence analysis using 476 salivary metagenomic datasets elucidates that these ECEs reside in 74% of the population. These ECEs, which we named, "Inocles", are giant plasmid-like circular genomic elements of 395 kb in length, including Streptococcus as a host bacterium. Inocles encode a series of genes that contribute to intracellular stress tolerance, such as oxidative stress and DNA damage, and cell wall biosynthesis and modification involved in the interactions with oral epithelial cells. Moreover, Inocles exhibit significant positive correlations with immune cells and proteins responding to microbial infection in peripheral blood. Intriguingly, we examine and find their marked reductions among 68 patients of head and neck cancers and colorectal cancers, suggesting its potential usage for a novel biomarker of gastrointestinal cancers. Our results suggest that Inocles potentially boost the adaptive capacity of host bacteria against various stressors in the oral environment.},
}

Humans
Saliva/microbiology
*Microbiota/genetics
Metagenomics/methods
*Mouth/microbiology
Female
Male
Colorectal Neoplasms/microbiology
Head and Neck Neoplasms/microbiology
Metagenome
Adult
DNA, Bacterial/genetics
*Bacteria/genetics
Middle Aged
Streptococcus/genetics

@article {pmid40788706,
year = {2025},
author = {Israel, A and Israel, S and Weizman, A and Ashkenazi, S and Vinker, S and Magen, E and Merzon, E},
title = {Atovaquone-proguanil and reduced digestive cancer risk: a Toxoplasma gondii connection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2545412},
pmid = {40788706},
issn = {1949-0984},
mesh = {Humans ; Middle Aged ; *Atovaquone/therapeutic use/pharmacology ; *Toxoplasma/isolation & purification/drug effects/genetics ; Adult ; Male ; Aged ; Female ; Retrospective Studies ; *Proguanil/therapeutic use/pharmacology ; Drug Combinations ; Gastrointestinal Microbiome/drug effects ; Feces/parasitology/microbiology ; *Colorectal Neoplasms/epidemiology/prevention & control/parasitology ; Toxoplasmosis ; Incidence ; Metagenomics ; },
abstract = {Emerging evidence suggests microbial pathogens contribute to digestive cancer risk. Atovaquone - proguanil (A-P), an antimalarial with antiparasitic activity, has been associated with a reduced risk of colorectal cancer (CRC). We conducted a retrospective cohort study using the TriNetX US Collaborative Network, including over 100,000 individuals aged 40-69 years who received A-P, matched 1:1 to controls who received other medications. Incident digestive cancers were analyzed using Cox proportional hazards models. Additionally, we performed a metagenomic analysis of 1,044 fecal samples from 156 individuals to assess the abundance of Toxoplasma gondii in CRC-associated microbiota. A-P use was associated with a significant reduction in digestive cancer incidence across all age groups: hazard ratios (HRs) ranged from 0.49 to 0.53 (all p < 0.001). Protective associations extended to pancreatic cancer (HR range, 0.50-0.72). In metagenomic analysis, T. gondii was the most discriminatory microbial species for CRC (p = 1.8 × 10[-16]), detected above threshold in 22.6% of CRC samples versus 1.6% of controls (odds ratio 18.2, 95% CI, 8.2-47.6, p = 2.3 × 10[-22]). These findings suggest T. gondii may be an overlooked microbial risk factor for digestive cancers, and that A-P may offer chemopreventive effects through antiparasitic activity. Prospective studies are needed to evaluate its preventive potential.},
}

Humans
Middle Aged
*Atovaquone/therapeutic use/pharmacology
*Toxoplasma/isolation & purification/drug effects/genetics
Adult
Male
Aged
Female
Retrospective Studies
*Proguanil/therapeutic use/pharmacology
Drug Combinations
Gastrointestinal Microbiome/drug effects
Feces/parasitology/microbiology
*Colorectal Neoplasms/epidemiology/prevention & control/parasitology
Toxoplasmosis
Incidence
Metagenomics

@article {pmid40785047,
year = {2025},
author = {Shi, H and Wu, M and Wu, X and Liu, Z and Jiang, S and Li, G and Yang, Y and Fu, Y and Wang, Q and Zhang, G and Cheng, L},
title = {Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2542384},
pmid = {40785047},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Atherosclerosis/microbiology/genetics/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Transcriptome ; Metabolomics ; Multiomics ; },
abstract = {Atherosclerosis (AS), a predominant contributor to global cardiovascular disease burden, exhibits complex interplay with gut microbiota dysbiosis. While the associations between microbial imbalance and AS pathogenesis are well-documented, the pathophysiological mechanisms governing microbe-host crosstalk remain incompletely characterized. Current research limitations stem from methodological heterogeneity across studies and the absence of consensus regarding disease-specific microbial signatures. In this study, we conducted an integrated multi-omics analysis to characterize the functional signatures of gut microbiome in AS. We collected all public AS-related 6 microbiome datasets and 8 peripheral blood host transcriptomic datasets from across the world, comprising 456 metagenomic samples and 111 16S rRNA gene sequencing samples for microbial profiling, alongside 118 RNA-Seq samples and 302 microarray samples. We systematically characterized AS microbial taxa and computationally inferred the metabolic potential for the gut microbiome using metabolomic-related data. Metabolite-host gene interactions were further predicted based on the synergistic effects between microbiome and host transcriptome in AS. Five "microbe-metabolite-host gene" tripartite associations related to AS were identified involving 5 microbial genera (Actinomyces, Bacteroides, Eisenbergiella, Gemella, and Veillonella), 2 metabolites (Ethanol and H2O2), and 2 host genes (FANCD2 and GPX2), and the reliability of these associations was validated. Five microbial genera demonstrated robust diagnostic potential as noninvasive biomarkers, with 5-fold cross-validation, study-to-study transfer validation, and leave-one-study-out (LOSO) validation confirming good diagnostic performance. Additionally, the specificity of the biomarkers was validated against hypertension, inflammatory bowel disease (IBD), diabetes, and obesity cohorts. Our study unveiled the functional characteristics of gut microbiota interacting with AS host genes and highlighted the potential of gut microbiota as both diagnostic biomarkers and therapeutic targets for AS. However, the findings should be interpreted considering the inherent heterogeneity of the integrated datasets and the preliminary diagnostic value of the biomarkers.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Atherosclerosis/microbiology/genetics/metabolism
*Bacteria/classification/genetics/isolation & purification/metabolism
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Transcriptome
Metabolomics
Multiomics

@article {pmid40784769,
year = {2025},
author = {Kim, HS and Kim, BH and Nam, B and Oh, SJ and Park, SK and Lee, SW and Lee, JY and Jo, S and Lee, YA and Lee, JY and Park, DI and Kim, TH and Lee, CK},
title = {Oral-gut microbiome axis in a Korean cohort with inflammatory bowel disease and ankylosing spondylitis (INTEGRATE): a prospective and observational study protocol.},
journal = {BMJ open},
volume = {15},
number = {8},
pages = {e092075},
pmid = {40784769},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; *Spondylitis, Ankylosing/microbiology ; Republic of Korea ; Observational Studies as Topic ; *Crohn Disease/microbiology ; RNA, Ribosomal, 16S ; *Inflammatory Bowel Diseases/microbiology ; Female ; Adult ; *Mouth/microbiology ; Dysbiosis ; Male ; *Colitis, Ulcerative/microbiology ; Saliva/microbiology ; },
abstract = {INTRODUCTION: The global burden of chronic immune-mediated inflammatory diseases (IMIDs) is increasing, and rising prevalence rates significantly affect socioeconomic factors and quality of life. Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), along with ankylosing spondylitis (AS), are prominent chronic IMIDs that share overlapping pathophysiological mechanisms. Recent research has highlighted the importance of the gut microbiota in the pathogenesis of these diseases, suggesting that shared microbial dysbiosis may contribute to their development. Comprehensive research focusing on the gut and oral microbial characteristics and environmental factors is essential to elucidate the fundamental pathophysiology and develop personalised management strategies for IBD and AS. In-depth analyses and insights based on multiomics approaches are required to achieve these objectives.

METHODS AND ANALYSIS: This protocol describes a nationwide prospective observational study of CD, UC and AS in a Korean population. Over 5 years, we aim to recruit at least 900 patients with IBD and 200 first-degree relatives (FDRs), 500 patients with AS and 200 of their FDRs, and 2244 healthy controls. We will systematically collect clinical data and biological samples, including saliva, stool, blood and tissue biopsies, for integrative multiomics analyses focusing primarily on the microbiome. Highly advanced full-length 16S ribosomal RNA gene sequencing and shotgun metagenomics will be used to characterise the microbial composition of saliva and stool samples. Quantitative microbiome profiling will be used to address the pathological, physiological and ecological differences between microbial groups that may be masked by their relative abundance. Metabolomic analyses will be conducted on saliva, stool and plasma samples to assess functional metabolic profiles. Culturomics will be used to isolate, identify and characterise the diversity of microbial species, including rare or previously unrecognised species, to provide a comprehensive understanding of the microbiota associated with these diseases.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the Ethics Committee of Kyung Hee University Hospital, Hanyang University Hospital, Kangbuk Samsung Hospital, Yeungnam University Hospital, Kyungpook National University Hospital, Chonnam National University Hospital, Wonkwang University Hospital, Catholic University Daejeon St. Mary's Hospital, Soon Chun Hyang University Hospital Cheonan, Chung-Ang University Hospital, Inje University Haeundae Paik Hospital, Dankook University Hospital, Hanyang University Guri Hospital, Kyung Hee University Hospital at Gangdong, Chung-Ang University Gwangmyeong Hospital and Keimyung University Dongsan Hospital. Our research team will provide detailed information about the study, including an information sheet explaining its aims and procedures, prior to enrolment. Prospective participants will be informed that they have the right to withdraw from the study at any time, without penalty. Participants will be assured of the anonymity and confidentiality of any data they provide throughout the study, using participant numbers and the storage of sensitive data in locked cabinets. Participants will be enrolled in the study only after providing written informed consent to the research staff. The results of this study will be disseminated to healthcare and academic professionals through publications in peer-reviewed journals and presentations at international conferences.

TRIAL REGISTRATION NUMBER: This prospective observational study is registered at ClinicalTrials.gov ((ID: NCT06124833, data first posted: 9 November 2023); (ID: NCT06076083, data first posted: 21 November 2023) and (ID: NCT06183697, data first posted: 27 December 2023)).},
}

Humans
*Gastrointestinal Microbiome
Prospective Studies
*Spondylitis, Ankylosing/microbiology
Republic of Korea
Observational Studies as Topic
*Crohn Disease/microbiology
RNA, Ribosomal, 16S
*Inflammatory Bowel Diseases/microbiology
Female
Adult
*Mouth/microbiology
Dysbiosis
Male
*Colitis, Ulcerative/microbiology
Saliva/microbiology

@article {pmid40783398,
year = {2025},
author = {Shen, Y and Sun, D and Chen, K and Jiang, J and Shao, D and Yang, L and Sun, C and Liu, D and Ke, Y and Wu, C and Walsh, TR and Shen, J and Lv, Z and Wang, Y},
title = {High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {156},
pmid = {40783398},
issn = {2055-5008},
support = {81991535//National Natural Science Foundation of China/ ; 32141002//National Natural Science Foundation of China/ ; 2022YFD1800400//National Key Research and Development Program of China/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Dietary Fiber/administration & dosage ; *Diet, High-Fat ; Mice ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Metagenomics/methods ; Male ; Humans ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Interspersed Repetitive Sequences ; Female ; },
abstract = {Antimicrobial resistance (AMR) is a global health challenge. The gut microbiome, a major reservoir for AMR, is influenced by dietary habits. However, the specific impact of dietary patterns on gut resistome remains poorly understood. This study aimed to assess the effects of high-fat/low-fiber and high-fiber/low-fat diets on the development of AMR in the gut microbiome. The shift from a normal diet to a high-fat/low-fiber or a high-fiber/low-fat diet in mice resulted in corresponding increases and decreases in the relative abundance of the resistome (0.14 to 0.25, p < 0.001 vs. 0.14 to 0.09 p < 0.05), virulence genes (VGs) (0.56 to 0.91, p < 0.001 vs. 0.58 to 0.50, p < 0.05), and mobile genetic elements (MGEs) (0.20 to 1.66, p < 0.001 vs. 0.22 to 0.13, p < 0.05), respectively. Network analyses identified bacteria such as Bacteroides, Parabacteroides, and Alistipes as hosts of ARGs and VGs, with changes in their abundance closely associated with shifts in ARG and VG levels. Mobile genetic elements such as Tn916, ISBf10, IS91, and intl1 were linked to these variations, including genes conferring resistance to vancomycin and capsule-related VGs. In humans, a similar trend was observed, with high-fat diets correlating with higher resistome levels, while high-fiber diets were associated with lower resistome levels compared to a normal diet group. ARGs were more prevalent in pathogenic genera such as Enterococcus spp., Klebsiella spp., Pseudomonas spp., and Staphylococcus spp. The high-fat/low-fiber diet increased the bacterial resistome and VG abundance compared to a high-fiber/low-fat diet. Therefore, adopting a high-fiber/low-fat diet may be an effective strategy to reduce the AMR burden in the human gut, providing a valuable insight for public health recommendations.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Animals
*Dietary Fiber/administration & dosage
*Diet, High-Fat
Mice
*Bacteria/genetics/drug effects/classification/isolation & purification
Metagenomics/methods
Male
Humans
Anti-Bacterial Agents/pharmacology
Feces/microbiology
Interspersed Repetitive Sequences
Female

@article {pmid40782126,
year = {2025},
author = {Andeta, AF and Lema, NK and Debel, GL and Misganaw, FW and Ifa, AC},
title = {Evaluating food safety of traditionally fermented kocho: microbial profiling through classical methods and PacBio SMRT sequencing technology.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {127},
pmid = {40782126},
issn = {1572-9699},
support = {CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; },
mesh = {*Fermented Foods/microbiology ; *Food Safety ; *Bacteria/classification/genetics/isolation & purification ; *Food Microbiology ; Ethiopia ; Fermentation ; Cross-Sectional Studies ; Fungi/isolation & purification/classification/genetics ; Microbiota ; },
abstract = {Enset (Ensete ventricosum) serves as a staple or co-staple food crop for over 20 million people in Southern, Southwestern, and Central Ethiopia, significantly contributing to regional food security. Despite its importance, food safety concerns surrounding its fermented product, kocho, remain largely unaddressed. This study aimed to evaluate the food safety of traditionally fermented kocho samples collected from districts in the Gamo Zone using a cross-sectional study design. The microbial community composition was analyzed through both culture-based methods and PacBio sequencing. The physicochemical properties exhibited slight variations in acidity, fermentation stage, and moisture content among samples from different districts. Culture-based microbiological analysis indicated total viable aerobic counts ranging from 5.76 to 7.13 log CFU/g, yeast and mold counts between 5.20 to 8.53 log CFU/g, and Enterobacteriaceae counts ranging from 5.03 to 6.13 log CFU/g. Metagenomic analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, with Acetobacter and Lactobacillus as the most prevalent genera. Notably, potential pathogenic bacteria, including Klebsiella pneumoniae, Klebsiella terrigena, Dysgonomonas capnocytophagoides, and Clostridium paraputrificum, were identified. The coexistence of beneficial microorganisms and potential pathogens underscores the urgent need for enhanced food safety measures in the traditional production of kocho.},
}

*Fermented Foods/microbiology
*Food Safety
*Bacteria/classification/genetics/isolation & purification
*Food Microbiology
Ethiopia
Fermentation
Cross-Sectional Studies
Fungi/isolation & purification/classification/genetics
Microbiota

@article {pmid40777923,
year = {2025},
author = {Ramos, SF and Siguenza, N and Zhong, W and Mohanty, I and Lingaraju, A and Richter, RA and Karthikeyan, S and Lukowski, AL and Zhu, Q and Nunes, WDG and Zemlin, J and Xu, ZZ and Hasty, J and Dorrestein, PC and Panda, S and Knight, R and Zarrinpar, A},
title = {Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects.},
journal = {Cell host & microbe},
volume = {33},
number = {7},
pages = {1057-1072},
pmid = {40777923},
issn = {1934-6069},
support = {R01 EB030134/EB/NIBIB NIH HHS/United States ; R01 HL148801/HL/NHLBI NIH HHS/United States ; I01 BX005707/BX/BLRD VA/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 CA236352/CA/NCI NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; R01 AI163483/AI/NIAID NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 CA265719/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; R01 DK136117/DK/NIDDK NIH HHS/United States ; R01 CA258221/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Circadian Rhythm ; Mice ; Cecum/microbiology ; *Transgenes ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; *Transcriptome ; Diet, High-Fat ; Metagenomics ; Metagenome ; Mice, Inbred C57BL ; Male ; *Bacteria/genetics/metabolism ; Gene Expression Profiling ; },
abstract = {Diurnal rhythmicity in the gut maintains gut integrity, circadian rhythms, and metabolic homeostasis. However, existing studies focus on microbial composition rather than transcriptional activity. To understand microbial functional dynamics, we characterize diurnal fluctuations in the mouse cecal metatranscriptome and metagenome under high-fat diet and time-restricted feeding (TRF). We show that metatranscriptomics uncover TRF-induced time-dependent microbial functional shifts that are undetectable with metagenomics alone. We also found bile salt hydrolase (bsh) from Dubosiella newyorkensis exhibits diurnal expression in the TRF group. Engineering this bsh, along with other candidates, into a native E. coli chassis reveals distinct differences in deconjugation and amidation activities, underscoring functional specificity. In vivo, a D. newyorkensis bsh improves insulin sensitivity, glucose tolerance, and body composition, suggesting a direct role in TRF metabolic benefits. This study highlights how coupling metatranscriptomics with engineered bacterial systems is a powerful approach for uncovering time-dependent bacterial functions related to health and disease.},
}

Animals
*Circadian Rhythm
Mice
Cecum/microbiology
*Transgenes
Escherichia coli/genetics/metabolism
*Gastrointestinal Microbiome/genetics
*Transcriptome
Diet, High-Fat
Metagenomics
Metagenome
Mice, Inbred C57BL
Male
*Bacteria/genetics/metabolism
Gene Expression Profiling

@article {pmid40776036,
year = {2025},
author = {Upadhyay, U and Dhar, E and Bomrah, S and Syed-Abdul, S},
title = {Unraveling the Role of Gut Microbiota in Colorectal Cancer: A Global Perspectives and Biomarkers as Early Screening Tool for Colorectal Cancer.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1145-1149},
doi = {10.3233/SHTI251018},
pmid = {40776036},
issn = {1879-8365},
mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; *Biomarkers, Tumor ; Metagenomics ; },
abstract = {Colorectal cancer (CRC), the second deadliest cancer globally, is closely tied to gut microbiota, opening doors for early detection and treatment. This review of 45 studies (2018-2024) highlights microbial biomarkers like Fusobacterium nucleatum, Bacteroides fragilis, and Parvimonas micra, with strong diagnostic accuracy (AUC >80%) across populations. Techniques like 16S rRNA sequencing, metagenomics, and shotgun sequencing revealed these links. Gut-based diagnostics offer a non-invasive, cost-effective alternative to colonoscopy and FIT for spotting early CRC and precancerous lesions. Yet, regional microbial differences and inconsistent methods-sample processing and sequencing-hinder comparability. Standardizing approaches and exploring fungi and viruses are key to unlocking microbiota's full potential in CRC prevention, diagnosis, and therapy.},
}

*Colorectal Neoplasms/diagnosis/microbiology
Humans
*Gastrointestinal Microbiome
*Early Detection of Cancer/methods
*Biomarkers, Tumor
Metagenomics

@article {pmid40775451,
year = {2025},
author = {Crognale, S and Amalfitano, S and Casentini, B and Di Pippo, F and Fazi, S and Tonanzi, B and Rossetti, S},
title = {Microbial signature of groundwater mixing in geothermal areas: insights from the Cimino-Vico volcanic system (central Italy).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28941},
pmid = {40775451},
issn = {2045-2322},
support = {CN_00000033//Ministero dell'Università e della Ricerca/ ; CN_00000033//Ministero dell'Università e della Ricerca/ ; },
mesh = {*Groundwater/microbiology ; Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Hot Springs/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The complex structure and dynamics of geothermal ecosystems strongly affect the spatial distribution and activity of aquatic microbial communities. The interactions between groundwaters and thermal waters represent an additional selective factor. A deeper understanding of microbial diversity, metabolic potential, and ecological interactions in groundwater mixing zones is essential for evaluating their impact on biogeochemical cycles (such as sulfur, nitrogen, and carbon) and predicting the ecological consequences of water mixing on ecosystem functioning. In this study, the taxonomic diversity and metabolic potentialities of microbial communities in groundwater and thermal waters revealed the occurrence of novel thermophiles able to cope with extreme physical-chemical conditions and high concentrations of toxic elements, such as arsenic, characteristics of the studied area. Furthermore, a core microbiome composed of the families Burkholderiaceae, Caulobacteraceae, Halothiobacillaceae, and Sulfurovaceae was identified as markers of the interaction between the two water compartments. Our findings emphasize the key role of microbial communities in S-, As-, and N-related biogeochemical cycles of geothermal areas.},
}

*Groundwater/microbiology
Italy
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Water Microbiology
*Hot Springs/microbiology
Ecosystem
RNA, Ribosomal, 16S/genetics

@article {pmid40774824,
year = {2025},
author = {Lee, I and Kim, BS and Suk, KT and Lee, SS},
title = {Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2406017},
pmid = {40774824},
issn = {1738-8872},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; Humans ; Fecal Microbiota Transplantation ; *Enterobacteriaceae Infections/prevention & control/microbiology/therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; Carbapenems/pharmacology ; Antimicrobial Stewardship ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) represent a critical antimicrobial resistance threat due to their resistance to last-resort antibiotics and high transmission potential. While conventional strategies-such as infection control, antimicrobial stewardship, and novel antibiotic development-remain essential, growing attention has shifted toward the gut microbiome, which plays a central role in mediating colonization resistance against CRE. Disruption of the intestinal microbiota-primarily driven by antibiotic exposure and further exacerbated by non-antibiotic drugs such as proton pump inhibitors-reduces microbial diversity and impairs functional integrity, facilitating CRE acquisition, prolonged carriage, and horizontal transmission. In response, microbiome-based strategies-including microbiome disruption indices (MDIs), fecal microbiota transplantation (FMT), and rationally designed symbiotic microbial consortia-are being explored as novel approaches for CRE prevention and decolonization. Mechanistic studies have shown that colonization resistance is mediated by both direct mechanisms (e.g., nutrient competition, short-chain fatty acid production) and indirect mechanisms (e.g., immune modulation via IL-36 signaling). Advances in metagenomics, metabolomics, and culturomics have enabled high-resolution profiling of gut microbial communities and their functional roles. Emerging preclinical and clinical evidence supports the potential of microbiome-informed interventions to predict infection risk, enhance antimicrobial stewardship, and guide the development of next-generation probiotics targeting CRE. Longitudinal studies continue to evaluate the efficacy of FMT and synthetic microbial consortia in eradicating intestinal CRE colonization. Collectively, these insights underscore the promise of gut microbiome science as a complementary and innovative strategy for CRE control in the post-antibiotic era.},
}

*Gastrointestinal Microbiome/drug effects
*Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology
Humans
Fecal Microbiota Transplantation
*Enterobacteriaceae Infections/prevention & control/microbiology/therapy
Anti-Bacterial Agents/pharmacology/therapeutic use
Animals
Carbapenems/pharmacology
Antimicrobial Stewardship

@article {pmid40772811,
year = {2025},
author = {Ascari, R and Migliorati, S and Ongaro, A},
title = {A New Dirichlet-Multinomial Mixture Regression Model for the Analysis of Microbiome Data.},
journal = {Statistics in medicine},
volume = {44},
number = {18-19},
pages = {e70220},
pmid = {40772811},
issn = {1097-0258},
support = {2022CLTYP4//Ministero dell'Università e della Ricerca/ ; },
mesh = {Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Monte Carlo Method ; *Models, Statistical ; Regression Analysis ; *Microbiota ; Multivariate Analysis ; Metagenomics ; },
abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this paper introduces a novel mixture distribution for multivariate counts and a regression model built upon it. The flexibility and interpretability of the proposed distribution accommodate both negative and positive dependence among taxa and are accompanied by numerous theoretical properties, including explicit expressions for inter- and intraclass correlations, thereby providing a powerful tool for understanding complex microbiome interactions. Furthermore, the regression model based on this distribution facilitates the clear identification and interpretation of relationships between taxa and covariates by modeling the marginal mean of the multivariate response (i.e., taxa counts). Inference is performed using a tailored Hamiltonian Monte Carlo estimation method combined with a spike-and-slab variable selection procedure. Extensive simulation studies and an application to a human gut microbiome dataset highlight the proposed model's substantial improvements over competing models in terms of fit, interpretability, and predictive performance.},
}

Humans
Computer Simulation
*Gastrointestinal Microbiome
Monte Carlo Method
*Models, Statistical
Regression Analysis
*Microbiota
Multivariate Analysis
Metagenomics

@article {pmid40772300,
year = {2025},
author = {Li, S and Huang, W and Ma, B and Xia, L and Hu, H and Sun, Y and Ni, H and Yuan, MM and Zhou, J and Zhang, J and Liang, Y},
title = {Viral Diversity Mediates Carbon Allocation for Ecosystem Multifunctionality Across Biomes.},
journal = {Global change biology},
volume = {31},
number = {8},
pages = {e70412},
doi = {10.1111/gcb.70412},
pmid = {40772300},
issn = {1365-2486},
support = {42425703//National Natural Science Foundation of China/ ; 2024QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; YSBR-108//CAS (Chinese Academy of Sciences) Project for Young Scientists in Basic Research/ ; ISSASIP2201//Innovation Program of Institute of Soil Science/ ; 2022ZB467//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {*Carbon/metabolism ; *Soil Microbiology ; *Ecosystem ; *Viruses/classification/genetics ; Metagenome ; Soil/chemistry ; Biodiversity ; },
abstract = {Viral diversity is essential for regulating the stability of ecosystem function by modulating the biochemical cycles via alterations in the survival and metabolic processes of host organisms. However, how viral survival strategies impact ecosystem function remains unresolved. Here, we analyzed 1824 metagenomes from soils across eight biomes, revealing that lytic viruses constituted a dominant proportion (88%) of the viral communities, with Siphoviridae (35.34%) being the most abundant lytic viral group. Viral communities significantly impacted soil organic carbon dynamics, while ecosystem multifunctionality was notably influenced by microbial necromass carbon, microbial biomass carbon, and various environmental factors. Microbial carbon use efficiency was the primary driver of ecosystem multifunctionality, with significant modulation by lytic and lysogenic viral communities, and lytic viruses contributed more directly to ecosystem multifunctionality (3%) compared to lysogenic viruses (1%). Our study underscores the pivotal role of viral communities, particularly lytic viruses, in shaping global carbon dynamics and ecosystem function, thereby providing a novel framework for future carbon management.},
}

*Carbon/metabolism
*Soil Microbiology
*Ecosystem
*Viruses/classification/genetics
Metagenome
Soil/chemistry
Biodiversity

@article {pmid40770776,
year = {2025},
author = {Kauer, L and Sapountzis, P and Imholt, C and Berens, C and Kuehn, R},
title = {Microbial exchange at the wildlife-livestock interface: insights into microbial composition, antimicrobial resistance and virulence factor gene dynamics in grassland ecosystems.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {84},
pmid = {40770776},
issn = {2524-4671},
abstract = {The transmission of antimicrobial resistance genes (ARGs) and virulence factors (VFs) between wildlife and livestock is an emerging concern for animal and human health, especially in shared ecosystems. ARGs enhance bacterial survival against antibiotics, while VFs contribute to infection processes, and the microbiome composition influences host health. Understanding microbial exchange at the wildlife-livestock interface is essential for assessing risks to both animal and human health. This study addresses the gap in knowledge by investigating the microbial composition, ARGs, and VFs in fecal matter from livestock (Bos taurus, Ovis aries) and wildlife (Microtus arvalis) cohabiting grassland pastures. Sampling was conducted within the DFG Biodiversity Exploratories, which provides valuable and extensive long-term ecological datasets and enables the study of diverse environmental parameters. Using metagenomic sequencing and 16 S rRNA amplicon analysis, we compared bacterial diversity, antimicrobial resistance profiles, and virulence gene presence across the three host species. Metagenomic analysis revealed host-specific differences in bacterial community composition. Livestock samples exhibited higher microbial diversity than those from M. arvalis, likely due to greater environmental exposure and management practices. The most common VFs in livestock were associated with immune modulation, whereas motility-related VFs were prevalent in M. arvalis. ARG profiles differed among hosts, suggesting rare events rather due to environmental acquisition than direct transmission between the hosts. The limited numbers of ARGs and VFs shared between the species indicate that horizontal gene transfer events between wildlife and livestock are infrequent. Notably, M. arvalis harbored diverse ARGs, including resistance to tetracycline and vancomycin, which were likely acquired from the environment rather than from direct livestock contact. These findings highlight the significant role of environmental reservoirs in shaping microbial communities and the spread of resistance. This research underscores the need for enhanced surveillance and ecosystem management strategies to mitigate the risk associated with antimicrobial resistance and the potential impacts on both animal and human health.},
}

@article {pmid40770684,
year = {2025},
author = {Winand, R and D'hooge, E and Van Uffelen, A and Bogaerts, B and Van Braekel, J and Hoffman, S and Roosens, NHCJ and Becker, P and De Keersmaecker, SCJ and Vanneste, K},
title = {Investigating fungal diversity through metabarcoding for environmental samples: assessment of ITS1 and ITS2 Illumina sequencing using multiple defined mock communities with different classification methods and reference databases.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {729},
pmid = {40770684},
issn = {1471-2164},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *High-Throughput Nucleotide Sequencing ; *Biodiversity ; *DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; Software ; Computational Biology/methods ; DNA, Fungal/genetics ; Sequence Analysis, DNA ; },
abstract = {An important challenge in taxonomic classification of environmental samples is capturing the real diversity by identifying all species present in a sample. Metabarcoding approaches are often employed to identify species in complex samples. The internal transcribed spacer (ITS) region is the official, widely adopted, barcode for identifying fungal species. Metabarcoding can be done in many different ways with multiple choices at different steps of the workflow. We present a comparative evaluation of the sequenced region (ITS1 and/or ITS2), two different reference databases (UNITE versus BCCM/IHEM), two different bioinformatics software packages (BLAST versus mothur), and the considered taxonomic level (species versus genus level), to accurately capture the diversity using 37 fungal defined mock communities (DMCs). The DMCs cover a broad range of fungal diversity, including 42 Ascomycota species (26 genera), 4 Basidiomycota species (4 genera), and 5 Mucoromycota species (5 genera), all commonly found in indoor environments in Western Europe. Classification performance was first evaluated using ITS1 and ITS2 sequences of all species in the DMCs, generated by Sanger sequencing, to evaluate the discriminatory power of ITS and set a baseline for subsequent comparison with Illumina sequencing. Classification performance was found to be variable depending on all considered variables (sequencing technology, taxonomic level, ITS region, software, database) with 56-100% of species correctly assigned. Sanger sequencing showed that neither ITS1 nor ITS2 resulted in optimal performance due to its low discriminatory power within certain genera. Compared to Sanger sequencing, Illumina sequencing generally resulted in lower precision but comparable recall. Classification performance was generally good at genus but not at species level, although intermediate taxonomic levels could present adequate alternatives. ITS2 typically resulted in slightly better precision and comparable recall compared to ITS1. The employed reference database had a marked effect, with BCCM/IHEM performing better than UNITE due to the difference in number of sequences in each database. BLAST resulted in better performance, but required expert curation, whereas mothur performed better when using an automated workflow. Estimating species abundances using Illumina sequencing read counts generally performed only poorly, although read abundance filtering could increase the precision of ITS1, but not ITS2. Each approach comes with its own advantages and inconveniences and should be carefully selected based on the objectives of the analysis. Our results highlight the power of metabarcoding using Illumina sequencing for investigating fungal diversity in complex samples and can guide scientists in selecting the most appropriate setup for their own purposes.},
}

*DNA Barcoding, Taxonomic/methods
*Fungi/genetics/classification
*High-Throughput Nucleotide Sequencing
*Biodiversity
*DNA, Ribosomal Spacer/genetics
Databases, Genetic
Software
Computational Biology/methods
DNA, Fungal/genetics
Sequence Analysis, DNA

@article {pmid40770608,
year = {2025},
author = {Babalola, OO and Shittu, OE and Enagbonma, BJ},
title = {Unveiling the Allium ampeloprasum rhizosphere microbiome and its functional dataset under different fertilization systems.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {54},
pmid = {40770608},
issn = {2730-6844},
support = {CRP/ZAF22-03//NRF, South Africa and ICGEB, Italy/ ; },
mesh = {*Rhizosphere ; *Allium/microbiology ; *Microbiota ; Metagenomics ; Fertilizers ; Soil Microbiology ; Bacteria/genetics/classification ; },
abstract = {Leek (Allium ampeloprasum) is a nutritious vegetable popularly cultivated in South Africa and most regions of the world. It is generally recognised as a source of vitamins and vegetables. Nevertheless, little is known about its rhizosphere microbiome and its microbial functional dataset under various fertilization systems. Therefore, this study intended to unveil the rhizosphere microbiome of Allium ampeloprasum and their functional datasets through shotgun metagenomics sequencing analysis.},
}

*Rhizosphere
*Allium/microbiology
*Microbiota
Metagenomics
Fertilizers
Soil Microbiology
Bacteria/genetics/classification

@article {pmid40770383,
year = {2025},
author = {Zhou, Z and Niu, Y and Ma, Y and Zhang, D and Wang, Y and Ji, R and Zhao, J and Ma, C and Zhu, H and Liu, Y and Tu, L and Lu, J and Zhang, B and Zhang, H and Ma, X and Chen, P},
title = {Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {181},
pmid = {40770383},
issn = {2049-2618},
support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//The Lanzhou Municipal Science and Technology Program/ ; 20250260006//the College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; },
mesh = {*Fusobacterium nucleatum/drug effects ; Animals ; Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology/drug therapy ; Mice ; Feces/microbiology ; *Fusobacterium Infections/microbiology ; Bifidobacterium/genetics ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Male ; Amidohydrolases/metabolism/genetics ; Bile Acids and Salts/metabolism ; Female ; Cell Proliferation ; Escherichia coli/genetics ; Cell Line, Tumor ; Disease Models, Animal ; },
abstract = {BACKGROUND: Fusobacterium nucleatum (F. nucleatum) is prevalent in colorectal cancer (CRC), and it can promote proliferation and induce chemoresistance via multiple pathways. The development of treatment strategies for F. nucleatum-infected CRC is of great importance.

METHODS: Shotgun metagenomic and metabolomic analyses of human feces, as well as metabolomic analysis of human blood, were performed to reveal the dysbiosis and metabolic dysregulation in CRC. Furthermore, the effects of Bifidobacterium animalis (B. animalis) on F. nucleatum and CRC were assessed in vitro and in vivo. Using a mouse CRC model, the function of bile salt hydrolase (BSH) in B. animalis was verified through heterologous expression in Escherichia coli (E. coli). Bile acids and drug library screening experiments were performed to inhibit F. nucleatum and tumor proliferation.

RESULTS: We identified an increase in F. nucleatum, enrichment of lipid metabolites, and depletion of Bifidobacterium in CRC patients. Furthermore, B. animalis inhibited F. nucleatum and CRC cells growth in an acid-dependent manner and reduced F. nucleatum-induced tumor increasement in mice. Mechanistically, F. nucleatum caused lipid accumulation, exacerbated inflammation, and intestinal barrier disruption, whereas B. animalis alleviated these changes, increased the Simpson diversity index, reduced lipid metabolites, and altered secondary bile acid composition in mice. Moreover, E. coli-BSH and ursodeoxycholic acid (UDCA) inhibited F. nucleatum-induced lipid accumulation and FASN/CPT1/NF-κB upregulation. Additionally, they alleviated F. nucleatum-related intestinal tumorigenesis in vivo. Targeting F. nucleatum-infected CRC cells and subcutaneous tumors in mice, penfluridol or the combination of orlistat and 5-FU exhibited superior inhibitory effects compared to 5-FU alone.

CONCLUSIONS: F. nucleatum and lipid metabolites are enriched in CRC patients. Furthermore, BSH-expressing E. coli, UDCA, and penfluridol can alleviate F. nucleatum-induced lipid accumulation and tumor growth in mice. Video Abstract.},
}

*Fusobacterium nucleatum/drug effects
Animals
Humans
*Colorectal Neoplasms/microbiology/metabolism/pathology/drug therapy
Mice
Feces/microbiology
*Fusobacterium Infections/microbiology
Bifidobacterium/genetics
*Lipid Metabolism/drug effects
Gastrointestinal Microbiome
Dysbiosis/microbiology
Male
Amidohydrolases/metabolism/genetics
Bile Acids and Salts/metabolism
Female
Cell Proliferation
Escherichia coli/genetics
Cell Line, Tumor
Disease Models, Animal

@article {pmid40769940,
year = {2025},
author = {De Corte, D and Dlugosch, L and Srivastava, A and Simon, M and Hansell, DA and Bercovici, S and Orellana, M},
title = {Taxonomic and Functional Features of Surface to Deep-Sea Prokaryotic Communities in the Eastern North Pacific Ocean.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70170},
pmid = {40769940},
issn = {1758-2229},
support = {CO 2218/2-1//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; OCE-1634009//National Science Foundation/ ; OCE-1634250//National Science Foundation/ ; },
mesh = {Pacific Ocean ; *Seawater/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Archaea/classification/genetics/isolation & purification/metabolism ; Phylogeny ; *Microbiota ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {Biogeochemical cycles in the ocean are strongly influenced by microbial activity, which affects nutrient and organic matter cycling. These processes, influenced by factors such as temperature, salinity, density and inorganic nutrients, drive the vertical stratification of microbial communities, which subsequently influence the chemistry at different depth layers. Sequencing technology has expanded our understanding of oceanic prokaryotic communities' taxonomic and functional potential. However, there is limited information on how these communities vary across gradients. In this study, we conducted metagenomic analyses on samples from the eastern North Pacific, collected across a longitudinal transect around 45°N and throughout the entire water column. We assessed taxonomic and functional classification, focusing on the roles of prokaryotic communities in biogeochemical cycling. Our results revealed that the surface community was dominated by the SAR11 clade, followed by Flavobacterales and Rhodobacterales. The deep layers harboured a more diverse community, where Thaumarchaeota accounted for the most significant proportion. This clear taxonomic stratification led to variations in the communities' functional capabilities across different depth layers. Photosynthesis and heterotrophy dominated the surface layers, whereas the deeper layers exhibited a mix of metabolic features, allowing organisms to potentially utilise both inorganic and organic carbon sources.},
}

Pacific Ocean
*Seawater/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
*Archaea/classification/genetics/isolation & purification/metabolism
Phylogeny
*Microbiota
Metagenomics
RNA, Ribosomal, 16S/genetics
Metagenome

@article {pmid40767981,
year = {2025},
author = {Jena, R and Singh, NA and Ahmed, N and Choudhury, PK},
title = {Bifidobacteria in antibiotic-associated dysbiosis: restoring balance in the gut microbiome.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {297},
pmid = {40767981},
issn = {1573-0972},
mesh = {*Dysbiosis/chemically induced/microbiology/therapy ; Humans ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bifidobacterium/physiology ; *Anti-Bacterial Agents/adverse effects ; Animals ; Prebiotics ; },
abstract = {Antibiotic-associated dysbiosis disrupts the gut's microbial balance, leading to reduced diversity, overgrowth of antibiotic-resistant strains, and compromised gut homeostasis. This can result in inflammation, increased intestinal permeability, impaired immunity, and heightened susceptibility to infections. In this context, probiotics have been highlighted as a promising remedy in alleviating this antibiotic-induced gut microbiome aberrations with subsequent decrease of the detrimental effects. Bifidobacteria, a prominent bacterial group with promising probiotic attributes, have shown effectiveness in restoring the gut microbiome by strong adherence to the colon's mucosal lining and enhancing the immune response through increased anti-inflammatory cytokines. They also play a crucial role as key producers of acetic acid, which supports butyric acid-producing bacteria essential for colonocyte health during dysbiosis. The synergistic use of bifidobacteria with other probiotic species or prebiotic substrates has further enhanced their survival, colonization capacity, and overall impact on gut microbial restoration. Advanced metagenomic analyses have begun to reveal strain-specific functions, paving the way for personalized probiotic therapies tailored to an individual's unique microbiome profile. Despite encouraging progress, critical research gaps persist, particularly regarding strain-specific efficacy, formulation stability, long-term outcomes, underlying mechanisms, systemic interactions, and the distinct and specific role of bifidobacteria. Addressing these gaps through targeted clinical investigations is essential to fully harness their therapeutic potential and develop optimized strategies for restoring the microbial balance in the gut microbiome.},
}

*Dysbiosis/chemically induced/microbiology/therapy
Humans
*Probiotics/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Bifidobacterium/physiology
*Anti-Bacterial Agents/adverse effects
Animals
Prebiotics

@article {pmid40766845,
year = {2025},
author = {Zheng, N and Yu, HL and Zhang, BJ and Wang, D and Ji, YL and Dai, LL and Li, W and Li, SH and Hu, ZL and Zheng, YS},
title = {Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562965},
pmid = {40766845},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/virology ; *Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Lung/virology ; *Blood/virology ; Bacteria/classification/genetics/isolation & purification ; *Virus Diseases/virology ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.

METHODS: A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.

RESULTS: Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with Siphoviridae and Myoviridae as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as Haemophilus, Megasphaera, and Treponema as key bacterial hosts.

CONCLUSIONS: This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Bronchoalveolar Lavage Fluid/virology
*Virome/genetics
*Viruses/genetics/classification/isolation & purification
Female
Male
Middle Aged
Adult
Aged
*Lung/virology
*Blood/virology
Bacteria/classification/genetics/isolation & purification
*Virus Diseases/virology

@article {pmid40764903,
year = {2025},
author = {Jingwen, J and Jingran, F and Liye, M and Yu, H and Yancen, M and Jingya, Z},
title = {The role of cervical microbiome in cervical incompetence: insights from 16 S rRNA metagenomic sequencing.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {486},
pmid = {40764903},
issn = {1471-2180},
support = {No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; },
mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pregnancy ; Metagenomics ; Adult ; *Uterine Cervical Incompetence/microbiology/immunology ; *Bacteria/classification/genetics/isolation & purification ; *Cervix Uteri/microbiology ; NF-kappa B/metabolism ; Toll-Like Receptor 2/metabolism/genetics ; Toll-Like Receptor 4/metabolism/genetics ; Cervix Mucus/microbiology ; },
abstract = {Cervical incompetence (CI) is recognized as a critical factor contributing to mid-pregnancy miscarriage and preterm delivery, significantly affecting pregnancy outcomes. Despite this, the specific role of the microbiome in this pathological process remains inadequately understood. This study seeks to elucidate the core microbiome associated with CI in pregnant women and explore its potential biological mechanisms. Utilizing 16 S rRNA metagenomic sequencing, we examined the cervical mucus microbiota of women with CI both pre-operatively (PreOp) and post-operatively (PostOp). Subsequently, the immunomodulatory effects of these microbial communities on the immune system were systematically assessed using quantitative real-time PCR, Western blotting, and enzyme-linked immunosorbent assay. The findings revealed a significant reduction in microbial diversity and richness in PostOp cervical mucus, alongside notable alterations in microbiota composition. The genera Lactobacillus, Bifidobacterium, Gardnerella, Streptococcus, and Anaerococcus were identified as predominant. Further analysis demonstrated that treatment with 25% Lactobacillus crispatus (L. crispatus) supernatants, in comparison to 25% Group B Streptococcus (GBS) supernatants, resulted in high cell viability and normal morphology in HcerEpic cells. Importantly, the combination of 25% L. crispatus and 25% GBS supernatants significantly reduced the mRNA and protein expression levels of Toll-like receptor 4 (TLR4), Toll-like receptor 2 (TLR2), and nuclear factor kappa B (NF-κB) in vitro. These results indicate that L. crispatus may play a role in modulating cervical inflammation in CI by suppressing the TLR/NF-κB signaling pathway, potentially contributing to a more stable cervical microenvironment during pregnancy.},
}

Female
Humans
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Pregnancy
Metagenomics
Adult
*Uterine Cervical Incompetence/microbiology/immunology
*Bacteria/classification/genetics/isolation & purification
*Cervix Uteri/microbiology
NF-kappa B/metabolism
Toll-Like Receptor 2/metabolism/genetics
Toll-Like Receptor 4/metabolism/genetics
Cervix Mucus/microbiology

@article {pmid40761666,
year = {2025},
author = {Zhou, H and Mu, X and Hu, H and Zhao, S and Hu, N and Yang, M and Jiang, J},
title = {DHLCA Alleviates Diabetic Kidney Disease via TGR5/FXR Activation and Gut Microbiota Remodeling.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {6469-6485},
pmid = {40761666},
issn = {1177-8881},
mesh = {*Receptors, G-Protein-Coupled/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Diabetic Nephropathies/drug therapy/metabolism ; Animals ; Mice ; Male ; Humans ; *Receptors, Cytoplasmic and Nuclear/metabolism/agonists ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; Middle Aged ; Diabetes Mellitus, Experimental/drug therapy/metabolism ; Mice, Inbred C57BL ; Female ; *Lithocholic Acid/analogs & derivatives/pharmacology ; Disease Models, Animal ; },
abstract = {PURPOSE: Diabetic kidney disease (DKD) is a major contributor to chronic kidney disease worldwide. Bile acids (BAs) are increasingly recognized as key regulators of glucose metabolism and kidney function. This study aimed to investigate the role of BA metabolism in the progression of DKD.

METHODS: Plasma BA profiles were measured in healthy controls (HC), patients with type 2 diabetes mellitus (T2DM), and patients with DKD using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). After identifying potential BA biomarkers in the clinical cohort, in vivo validation was conducted using dehydrolithocholic acid (DHLCA) intervention in DKD mouse model. Kidney injury markers, as well as the expression of Takeda G protein-coupled receptor 5 (TGR5) and farnesoid X receptor (FXR), were evaluated. In addition, gut microbiota (GM) composition was analyzed via metagenomic sequencing following DHLCA treatment.

RESULTS: The plasma DHLCA levels were significantly lower in DKD with macroalbuminuria group compared to T2DM group and DKD with microalbuminuria group (P < 0.01). Partial Spearman correlation analysis adjusted for age and diabetes duration showed that DHLCA levels were negatively correlated with urine albumin (ρ = -0.347; 95% CI, -0.531 to -0.135; q = 0.008) and urine albumin-to-creatinine ratio (UACR) (ρ = -0.332; 95% CI, -0.499 to -0.155; q = 0.010). In vivo, DHLCA administration significantly reduced UACR and fasting blood glucose (FBG) levels (P < 0.01), and improved liver function (ALT, P < 0.05) in DKD mice. DHLCA treatment attenuated renal tubular injury, restored TGR5 and FXR expression in kidney tissue, and decreased levels of kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL). Metagenomic analysis revealed an enrichment of Lachnospiraceae bacterium following DHLCA treatment.

CONCLUSION: DHLCA may represent a promising therapeutic candidate for DKD by targeting the TGR5/FXR signaling pathway and GM remodeling. Its metabolic and kidney benefits, along with an improved hepatic profile and absence of hepatotoxicity, support further translational investigation.},
}

*Receptors, G-Protein-Coupled/metabolism
*Gastrointestinal Microbiome/drug effects
*Diabetic Nephropathies/drug therapy/metabolism
Animals
Mice
Male
Humans
*Receptors, Cytoplasmic and Nuclear/metabolism/agonists
*Diabetes Mellitus, Type 2/drug therapy/metabolism
Middle Aged
Diabetes Mellitus, Experimental/drug therapy/metabolism
Mice, Inbred C57BL
Female
*Lithocholic Acid/analogs & derivatives/pharmacology
Disease Models, Animal

@article {pmid40757481,
year = {2025},
author = {Bustos-Caparros, E and Viver, T and Gago, JF and Avontuur, JR and Amiour, S and Baxter, BK and Llames, ME and Mutlu, MB and Oren, A and Ramírez, AS and Stott, MB and Venter, SN and Santos, F and Antón, J and Rodriguez-R, LM and Bosch, R and Hedlund, BP and Konstantinidis, KT and Rossello-Mora, R},
title = {Global dominance of Haloquadratum walsbyi by a single highly clonal genomovar with distinct gene content and viral cohorts from close relatives.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf165},
pmid = {40757481},
issn = {1751-7370},
abstract = {Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > ANI > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.},
}

@article {pmid40755755,
year = {2025},
author = {Vicente-Valor, J and Tesolato, S and Gómez-Garre, D and Paz-Cabezas, M and Ortega-Hernández, A and Fernández-Hernández, C and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Rupérez, FJ and García, A and Torres, A and Iniesta, P},
title = {Identification of clinically relevant profiles in colorectal cancer through integrated analysis of bacterial DNA and metabolome in serum.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1562416},
pmid = {40755755},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/blood/diagnosis/microbiology/metabolism ; Male ; Female ; Middle Aged ; *Metabolome ; *DNA, Bacterial/blood/genetics ; Aged ; Cross-Sectional Studies ; *Biomarkers, Tumor/blood ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome ; Metabolomics/methods ; Adult ; Bacteria/genetics ; },
abstract = {INTRODUCTION: There is increasing evidence demonstrating the relationship between microbiota and colorectal cancer. Several studies have been published analyzing microbiota in tissues and feces from cancer patients; however, there are only a few publications investigating the clinical utility of serum microbiome from colorectal cancer patients. Our aim was to advance in the search for serum biomarkers for the diagnosis of colorectal cancer.

METHODS: We conducted a cross-sectional study assessing bacterial DNA and metabolomic profiles in 64 serum samples from subjects affected by colorectal cancer and controls. A metagenomic analysis of the bacterial 16S rRNA gene in serum was established, and serum metabolites were detected through an untargeted metabolic study based on Gas Chromatography-Quadruple Time-Of-Flight Mass Spectrometry with accurate mass.

RESULTS AND DISCUSSION: After integrating the data resulting from the bioinformatics and statistical analyses, we obtained different profiles in colorectal cancer population and controls, regardless of the subjects' age, gender and body mass index. Serum levels of Firmicutes and threonic acid were the most relevant characteristics that could help differentiate both groups, achieving an excellent predictive accuracy in this discovery cohort (area under the ROC curve = 0.95). Although these results should be validated in other cohorts through multicenter studies, we consider that our data could be relevant and applicable to the early diagnosis of colorectal cancer.},
}

Humans
*Colorectal Neoplasms/blood/diagnosis/microbiology/metabolism
Male
Female
Middle Aged
*Metabolome
*DNA, Bacterial/blood/genetics
Aged
Cross-Sectional Studies
*Biomarkers, Tumor/blood
RNA, Ribosomal, 16S/genetics
Gastrointestinal Microbiome
Metabolomics/methods
Adult
Bacteria/genetics

@article {pmid40755247,
year = {2025},
author = {Nadimpalli, ML and Sehgal, N and Rojas-Salvatierra, L and Gilman, RH and Earl, AM and Worby, CJ and Schwab, M and Pickering, AJ and Pajuelo, MJ},
title = {Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2541029},
pmid = {40755247},
issn = {1949-0984},
support = {KL2 TR002545/TR/NCATS NIH HHS/United States ; R01 AI108695/AI/NIAID NIH HHS/United States ; T32 ES012870/ES/NIEHS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Peru/epidemiology ; *beta-Lactamases/metabolism/genetics ; Infant ; Feces/microbiology ; Male ; *Enterobacteriaceae/genetics/enzymology/isolation & purification/classification ; Female ; Child, Preschool ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Metagenomics ; },
abstract = {Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low- and middle-income countries. Some children nevertheless remain never or rarely colonized during early life. Understanding how this protection is conferred could be helpful for designing future interventions to protect children's health. Here, we investigated whether differences in gut microbiome development could underlie differential susceptibility to ESBL-E gut colonization over time among children in peri-urban Lima. Weekly stool and daily surveys were collected from 345 children < 3 years old during a 2016-19 study of enteric infections. A subset of children (n = 12) was rarely gut-colonized with ESBL-E from 1-16 months of age. We performed short-read metagenomic sequencing of stool collected at 3, 6, 7, 9, 12, and 16 months from these children and a random subset of 42 frequently colonized children, and characterized differences in their exposures and gut microbiomes. No differences in gut taxa or functional pathways were identified over time, though children harbored differentially abundant taxa, more unique E. coli strains, and a higher abundance of blaCTX-M gene copies at ESBL-E-positive versus negative timepoints. Differing patterns of ESBL-E colonization over time among children in peri-urban Lima do not appear to be related to differences in gut microbiome development.},
}

Humans
*Gastrointestinal Microbiome
Peru/epidemiology
*beta-Lactamases/metabolism/genetics
Infant
Feces/microbiology
Male
*Enterobacteriaceae/genetics/enzymology/isolation & purification/classification
Female
Child, Preschool
*Enterobacteriaceae Infections/microbiology/epidemiology
Metagenomics

@article {pmid40755225,
year = {2025},
author = {Pan, Z and Walsh, CJ and Feehily, C and Nori, SRC and McAuliffe, FM and Cotter, PD and MacSharry, J and van Sinderen, D},
title = {Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2541033},
pmid = {40755225},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Breast Feeding ; *Milk, Human/microbiology ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; },
abstract = {The infant resistome, the collection of antimicrobial resistance genes (ARGs) of newborns, is critical for gut microbiota establishment. Using metagenomic sequencing data, we analyzed various 1-week and 1-month postpartum samples to study infant resistome establishment, ARG transmission, and its impact on functional redundancy of the microbiota. A total of 431 samples were analyzed; infant stools (1-week, n = 119; 1-month, n = 119), maternal stools (1-month postpartum, n = 120), and breastmilk (1-month postpartum, n = 73). Breastfeeding correlated with increased functional redundancy and altered bacterial-ARG co-occurrence networks in the infant resistome. Escherichia coli dominated early resistome dynamics with a higher abundance correlating with reduced functional redundancy. Bifidobacterium longum exhibited a consistent negative association with 21 ARGs at one-month in breastfed infants, while four negative relationships between ARGs and Bifidobacterium bifidum were observed in formula-fed infants. ARG transmission via breastmilk appears to be gene-specific, with the quinolone resistance gene sdrM likely transmitted under maternal antibiotic use. Delivery mode modulated the microbial environment in ways that interact with resistome structure and changing functional redundancy, particularly through genera like Staphylococcus and Streptococcus. These findings highlight the role of early feeding practices in resistome development and propose functional redundancy as a key ecological framework for understanding infant gut resistome dynamics.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
*Breast Feeding
*Milk, Human/microbiology
Infant
Female
Infant, Newborn
Anti-Bacterial Agents/pharmacology
Feces/microbiology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Drug Resistance, Bacterial/genetics
Metagenomics

@article {pmid40753386,
year = {2025},
author = {AlHilli, MM and Sangwan, N and Myers, A and Tewari, S and Lindner, DJ and Cresci, GAM and Reizes, O},
title = {The effects of dietary fat on gut microbial composition and function in a mouse model of ovarian cancer.},
journal = {Journal of ovarian research},
volume = {18},
number = {1},
pages = {174},
pmid = {40753386},
issn = {1757-2215},
support = {K12 CA076917/CA/NCI NIH HHS/United States ; K12CA076917//NIH K12CA076917 Clinical Oncology Training Program/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; *Ovarian Neoplasms/microbiology/pathology ; Mice ; Disease Models, Animal ; Humans ; *Dietary Fats/pharmacology ; Diet, Ketogenic ; Cell Line, Tumor ; Mice, Inbred C57BL ; Diet, High-Fat ; },
abstract = {OBJECTIVES: The gut microbiome (GM) is pivotal in regulating inflammation, immune responses, and cancer progression. This study investigates the effects of a ketogenic diet (KD) and a high-fat/low-carbohydrate (HF/LC) diet on GM alterations and tumor growth in a syngeneic mouse model of high-grade serous ovarian cancer (EOC).

METHODS: Thirty female C57BL/6 J mice injected with KPCA cells were randomized into KD, HF/LC, and low-fat/high-carbohydrate (LF/HC) diet groups. Tumor growth was monitored with live, in vivo imaging. Stool samples were collected at the time of euthanasia and analyzed by 16SrRNA sequencing and shotgun metagenomic sequencing was performed to identify differential microbial taxonomic composition and metabolic function.

RESULTS: Our findings revealed that KD and HF/LC diets significantly accelerated EOC tumor growth compared to the LF/HC diet in a xenograft model. GM diversity was markedly reduced in KD and HF/LC-fed mice, correlating with increased tumor growth, whereas LF/HC-fed mice showed higher GM diversity. Metagenomic analyses identified distinct alterations in microbial taxa including Bacteroides, Lachnospiracae bacterium, Bacterium_D16_50, and Enterococcus faecalis predominantly abundant in HF/LC-fed mice, Dubsiella_newyorkensis predominantly abundant in LF/HC-fed, and KD fed mice showing a higher abundance of Akkermansia and Bacteroides. Functional pathways across diet groups indicated polyamine biosynthesis and fatty acid oxidation pathways were enriched in HF/LC-fed mice.

CONCLUSIONS: These results highlight the intricate relationship between diet andthe gut microbiome in promoting EOC growth. The potential role of dietary interventions in cancer prevention and treatment warrants further investigation.},
}

Animals
Female
*Gastrointestinal Microbiome/drug effects
*Ovarian Neoplasms/microbiology/pathology
Mice
Disease Models, Animal
Humans
*Dietary Fats/pharmacology
Diet, Ketogenic
Cell Line, Tumor
Mice, Inbred C57BL
Diet, High-Fat

@article {pmid40753152,
year = {2025},
author = {Jiang, W and Li, Y and Yang, J and Tan, X and Tian, R and Ma, G and Wu, J and Zhang, J and Huang, Y and Liu, P and Yuan, M and Song, X and Luo, L and Zhou, X and Zuo, H and Wong, ML and Licino, J and Zheng, P},
title = {Chronic stress in mice: how gut bacteria influence gene activity in key brain neurons.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {262},
pmid = {40753152},
issn = {2158-3188},
support = {2024MD754023//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology/genetics ; Mice ; *Stress, Psychological/microbiology/metabolism/genetics ; *Neurons/metabolism ; *Hypothalamus/metabolism ; Male ; Disease Models, Animal ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; *Depressive Disorder, Major/microbiology ; Mice, Inbred C57BL ; },
abstract = {Major depressive disorder (MDD) is a serious mental disorder. Increasing evidence suggests that changes of gut microbiota are involved in pathogenesis of depression, yet the underlying mechanisms remains unknown. Here, chronic unpredictable mild stress (CUMS) mice model was constructed to mimic depression. We characterized the microbial composition and function of control, bedding exchange, and CUMS mice through 16S rRNA gene and metagenomic sequencing. Additionally, single-nucleus RNA sequencing (snRNA-seq) was used to compare the transcriptomic changes in the hypothalamus of these three groups. We found that replacing the bedding of CUMS mice with that of control mice could reverse the depressive-like behaviors. The microbial signatures of bedding exchange group trended towards the control group at the genus level. The abundance of g_norank_f_Muribaculaceae significantly increased in the bedding exchange group compared to CUMS group. Meanwhile, we found that the CUMS mice were characterized by cell-specific transcriptomic changes in hypothalamus. Notably, the transcriptomes of excitatory neurons in the hypothalamus were mainly affected, and these changes could be effectively reversed by bedding exchange treatment. The gene modules analysis revealed that the gut microbiota mainly modulated glyoxylate and dicarboxylate metabolism as well as arginine biosynthesis in hypothalamic excitatory neurons. Our findings provide new insights into the pathogenesis of depression.},
}

Animals
*Gastrointestinal Microbiome/physiology/genetics
Mice
*Stress, Psychological/microbiology/metabolism/genetics
*Neurons/metabolism
*Hypothalamus/metabolism
Male
Disease Models, Animal
Transcriptome
RNA, Ribosomal, 16S/genetics
*Depressive Disorder, Major/microbiology
Mice, Inbred C57BL

@article {pmid40751224,
year = {2025},
author = {Reinoso-Peláez, EL and Saura, M and González, C and Ramón, M and Calvo, JH and Serrano, M},
title = {The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {177},
pmid = {40751224},
issn = {2049-2618},
support = {RTI-2018-096487-R-C33//Ministerio de Ciencia, Innovación y Universidades/ ; },
mesh = {Female ; Animals ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Sheep/microbiology ; *Fertility ; *Bacteria/classification/genetics/isolation & purification ; Pregnancy ; Genomics ; Metagenome ; },
abstract = {BACKGROUND: Despite advancements in artificial insemination, sheep fertility rates remain suboptimal. Recent studies in other species highlight the critical role of reproductive microbiota in influencing fertility outcomes. This research explores the relationship between ovine vaginal microbiota, associated functional pathways, and fertility using advanced nanopore long-reading metagenomic sequencing on 297 ewes from three Spanish breeds across four herds. The study aimed to describe a core vaginal microbiota, analyse the complex interactions with herd, breed, age, and parity factors, and identify taxa and genes associated with reproductive success by artificial insemination.

RESULTS: The study identified Staphylococcus, Escherichia, and Histophilus as the most abundant genera. Microbial communities varied considerably between breeds and herds, with high predictive accuracy (> 90%) in classification models. Differential abundance analysis revealed that the genera Histophilus, Fusobacterium, Bacteroides, Campylobacter, Streptobacillus, Gemella, Peptoniphilus, Helococcus, Treponema, Tissierella, and Phocaeicola were more abundant in non-pregnant ewes. Some of these taxa were also associated with four COG entries and one KEGG orthologue significantly linked to non-pregnancy, primarily involving carbohydrate metabolism, defence mechanisms, and structural resilience. Age and parity were also associated with microbiota composition, particularly in ewes older than five years or with more than three parturitions, suggesting that cumulative physiological changes may contribute to microbial shifts over time.

CONCLUSIONS: The ewe's vaginal microbiome appears to be mainly influenced by both herd and breed, though distinguishing genetic from environmental factors is challenging within our study design. While the overall microbiota showed a subtle effect on pregnancy, certain genera had a significant negative impact, likely due to pathogenic or inflammatory properties that disrupt reproductive health. The metagenomic approach used here enabled not only comprehensive taxonomic classification but also detailed functional analysis, providing deeper insights into the microbiome's role in reproductive outcomes. Video Abstract.},
}

Female
Animals
*Vagina/microbiology
*Microbiota/genetics
*Metagenomics/methods
Sheep/microbiology
*Fertility
*Bacteria/classification/genetics/isolation & purification
Pregnancy
Genomics
Metagenome

@article {pmid40750823,
year = {2025},
author = {Adebayo, AA and Enagbonma, BJ and Babalola, OO},
title = {Comparative metagenomics on community structure and diversity of rhizomicrobiome associated with monoculture and soybean precedent carrot.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28161},
pmid = {40750823},
issn = {2045-2322},
mesh = {*Daucus carota/microbiology/growth & development ; *Glycine max/microbiology/growth & development ; Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Plant Roots/microbiology ; Biodiversity ; Agriculture/methods ; },
abstract = {Several studies have explored the impact of cropping systems, including monoculture and crop rotation, on the plant rhizosphere - an essential dynamic in designing strategies for optimizing soil health and crop productivity. It remains largely unknown how these agricultural practices drive the diversity and community structure of the microbiome in the carrot rhizosphere. Thus, this study aims to profile the core rhizo-microbiome of carrots grown under a monoculture system and those grown after soybean cultivation. The microbial DNA extracted from 12 soil samples collected from monoculture carrot rhizosphere (MCR), soybean-precedent carrot rhizosphere (SCR), and uncultivated land (bulk soils) (BS) were analyzed via shotgun metagenomics sequencing. Findings show that bacterial phyla were the most dominant taxa across the sampling points. Principal Component Analysis (PCA) revealed that Pseudomonadota, Bacillota, and Actinomycetota are significantly enriched in soybean-precedent carrot rhizosphere, monoculture carrot rhizosphere, and bulk soil, respectively. Furthermore, genera Bradyrhizobium and Agromyces were significantly enriched, and Rhodococcus was exclusively present in soybean-precedent carrot rhizosphere. Alpha and Beta diversity analyses indicated that the microbial community composition was unique within and between the sampling sites (genus level). Redundancy Analysis (RDA) demonstrated that soil properties like silt (contributing 84.2%), total nitrogen (contributing 83.2%), organic carbon (contributing 81.0%), and sand texture (contributing 75.8%) explained the variance in microbiome composition. This study provides fundamental insight into how cropping systems influence carrot rhizo-microbiome. Crop rotation practice with soybeans was found to increase microbial composition and diversity in carrot plantations.},
}

*Daucus carota/microbiology/growth & development
*Glycine max/microbiology/growth & development
Rhizosphere
*Metagenomics/methods
Soil Microbiology
*Microbiota/genetics
*Bacteria/genetics/classification
Plant Roots/microbiology
Biodiversity
Agriculture/methods

@article {pmid40748897,
year = {2025},
author = {Ségurel, L and Ulaganathan, TS and Mathieu, S and Loiodice, M and Poulet, L and Drouillard, S and Cygler, M and Helbert, W},
title = {The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329457},
pmid = {40748897},
issn = {1932-6203},
mesh = {Humans ; Asia, Eastern/ethnology ; Bacterial Proteins/genetics/metabolism ; *Bacteroides/enzymology/genetics ; *East Asian People/statistics & numerical data ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Glycoside Hydrolases/genetics/metabolism ; Metagenome ; Phylogeny ; *Polysaccharides, Bacterial/metabolism ; *Porphyra/microbiology ; Sepharose/analogs & derivatives ; },
abstract = {The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. An illustrative example of that is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates as well as metagenomic data from more than 14,000 worldwide individuals, we found that the porphyran PUL is present in 17 different Phocaeicola/Bacteroides species (including 12 species that were not known to carry it), as well as in two Parabacteroides species and two genera from the Bacillota phylum, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the prevalence of this porphyran PUL across 32 countries and showed that it exists in appreciable frequencies (>1%) only in East Asia (Japan, China, Korea). Finally, we identified three major PUL haplotypes which frequencies significantly differ between these East Asian countries. This geographic structure likely reflects the rate of bacterial horizontal transmission between individuals.},
}

Humans
Asia, Eastern/ethnology
Bacterial Proteins/genetics/metabolism
*Bacteroides/enzymology/genetics
*East Asian People/statistics & numerical data
*Gastrointestinal Microbiome/genetics
*Gene Transfer, Horizontal
Genetic Variation
Glycoside Hydrolases/genetics/metabolism
Metagenome
Phylogeny
*Polysaccharides, Bacterial/metabolism
*Porphyra/microbiology
Sepharose/analogs & derivatives

@article {pmid40748490,
year = {2025},
author = {He, T and Wang, Y and Zhao, L and Che, Y and Zhang, L and Zeng, Y and Shen, H and Hao, H and Cao, L},
title = {Integrated Microbiota-Bile Acid Analysis as Potential NonInvasive Biomarkers for Ulcerative Colitis Staging Diagnose.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {15},
pages = {e70859},
doi = {10.1096/fj.202501078R},
pmid = {40748490},
issn = {1530-6860},
support = {2021YFA1301300//the National Key Research and Development Program of China/ ; 2022YFF1100601//the National Key Research and Development Program of China/ ; 82173886//the National Natural Science Foundation of China/ ; 82373886//the National Natural Science Foundation of China/ ; 82404997//the National Natural Science Foundation of China/ ; G20582017001//111 Plan | Overseas Expertise Introduction Project for Discipline Innovation/ ; SKLNMZZ202402//the Project of State Key Laboratory of Natural Medicines, China Pharmaceutical University/ ; },
mesh = {Humans ; *Colitis, Ulcerative/diagnosis/microbiology/metabolism/blood ; *Bile Acids and Salts/metabolism/blood/analysis ; Male ; Biomarkers/metabolism/blood ; Adult ; Female ; Feces/microbiology/chemistry ; Middle Aged ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Clinical staging diagnosis and progression tracking for ulcerative colitis (UC) is as challenging as poor patient compliance with endoscopic biopsy. We perform a study that integrates metabolomic profiling, 16S rRNA, and metagenomic sequencing on serum and fecal samples from 23 active state UC patients, 24 remission state UC patients, and 20 healthy volunteers from China, aiming to explore a non-invasive integrative biochemical index to quantitatively track and monitor pathological activity of UC. Besides the known associations of microbes such as Fusobacterium nucleatum and Clostridium symbiosum with UC, we found several bile acid-transforming species, including 7α-dehydroxygenase and 7α/β-dehydrogenase expressing microbiota, were significantly correlated with UC pathological activity. We identified 2 bacterial gene markers related to secondary bile acid synthesis besides Clostridium scindens that differentiated active and remission stage UC and healthy control microbiomes. Relevantly, reduced serum deoxycholic acid (DCA)/cholic acid (CA) species ratio and increased fecal ursodeoxycholic acid (UDCA)/chenodeoxycholic acid (CDCA) ratio were associated with the pathological activity of UC. Moreover, receiver operating characteristic analysis based on serum/fecal bile acid ratios was much more accurate in the prediction of active and remission stage outcomes. This species-specific temporal change and bile acid dysregulation pattern linked to disease severity indicate that integrated microbiome-bile acid profiles may be implied for disease activity prediction and that targeting microbiome-mediated gut flora and bile acid homeostasis may be implicative of therapy efficacy. These insights will help improve clinical diagnosis and optimize existing medical treatments.},
}

Humans
*Colitis, Ulcerative/diagnosis/microbiology/metabolism/blood
*Bile Acids and Salts/metabolism/blood/analysis
Male
Biomarkers/metabolism/blood
Adult
Female
Feces/microbiology/chemistry
Middle Aged
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics

@article {pmid40746878,
year = {2025},
author = {Xu, F and Li, W and Zheng, XJ and Hao, Y and Yang, YH and Yang, H and Zhang, S and Cao, WX and Li, XX and Zhang, X and Du, GH and Ji, TF and Wang, JH},
title = {3-O-Acetyl-11-Keto-β-Boswellic Acid Suppresses Colitis-Associated Colorectal Cancer by Inhibiting the NF-Kb Signaling Pathway and Remodeling Gut Microbiota.},
journal = {Oncology research},
volume = {33},
number = {8},
pages = {1969-1989},
pmid = {40746878},
issn = {1555-3906},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Humans ; *Triterpenes/pharmacology ; *NF-kappa B/metabolism ; Signal Transduction/drug effects ; *Colitis-Associated Neoplasms/drug therapy/pathology/metabolism/microbiology ; Cell Proliferation/drug effects ; Apoptosis/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Colitis/complications/drug therapy ; Disease Models, Animal ; Cell Line, Tumor ; Male ; HCT116 Cells ; },
abstract = {OBJECTIVES: Colorectal cancer (CRC) is one of the most common cancers all over the world. The progression of CRC is associated with inflammation and disruptions in intestinal flora. 3-O-Acetyl-11-keto-β-boswellic acid (AKBA) has been noted for its potent anti-inflammatory properties. However, the effect of AKBA on colon cancer caused by inflammation and its mechanism are not unclear. The study is to explore the effect of AKBA on CRC and its mechanism.

MATERIALS AND METHODS: Cell proliferation, (5-ethynyl-2[']-deoxyuridine, EdU)-DNA synthesis assay and colony formation were used to assess the effect of AKBA on the proliferation of CRC cells. Flow cytometry was employed to analyze the cell cycle and apoptosis rate of cells treated with AKBA. RNA sequencing was done to explore the underlying mechanisms of AKBA. Western blot was used to assess the expression of key proteins in the nuclear factor kappa-B (NF-κB) signaling pathway after the treatment of AKBA. Real-time quantitative PCR (RT-qPCR), enzyme-linked immunosorbent assay (ELISA), and Meso Scale Discovery (MSD) assays were employed to check the anti-inflammation effects of AKBA on Lipopolysaccharide (LPS)-induced RAW264.7 cells and LPS-induced mouse model. Additionally, the Azoxymethane/Dextran sulfate sodium (AOM/DSS)-induced colitis-associated CRC model was used to evaluate the anti-CRC effect of AKBA. Gut microbiota profiling of fecal samples from CRC mice, both with and without AKBA treatment, was conducted through metagenomic sequencing analysis.

RESULTS: Our results showed that AKBA reduced the proliferation of HCT116 and SW620 cells, increased apoptosis of cells, and arrested the cell cycle at the G2/M phase. Results from RNA-seq showed that AKBA inhibited CRC by inhibiting the NF-κB signaling pathway and reducing cellular inflammation. Furthermore, AKBA reduced the levels of inflammatory cytokines, including tumor necrosis factor-α (TNF-α), Interferon-γ (IFN-γ), Interleukin-IL-12p70 (IL-12p70), Interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) in both the spleen and serum of LPS-induced acute inflammation mice. Additionally, AKBA inhibited the development of AOM/DSS-induced colitis-associated colon cancer in mice and positively influenced gut microbiota.

CONCLUSION: This study highlights the inhibitory effect of AKBA on colitis-associated CRC and reveals a novel aspect of its role in the remodeling of gut microbiota. These findings suggest that AKBA may be used as a potential therapeutic agent for CRC.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
Humans
*Triterpenes/pharmacology
*NF-kappa B/metabolism
Signal Transduction/drug effects
*Colitis-Associated Neoplasms/drug therapy/pathology/metabolism/microbiology
Cell Proliferation/drug effects
Apoptosis/drug effects
*Colorectal Neoplasms/drug therapy/pathology
*Colitis/complications/drug therapy
Disease Models, Animal
Cell Line, Tumor
Male
HCT116 Cells

@article {pmid40745465,
year = {2025},
author = {Popova, A and Rācenis, K and Brīvība, M and Saksis, R and Saulīte, M and Šlisere, B and Berga-Švītiņa, E and Oļeiņika, K and Saulīte, AJ and Seilis, J and Kroiča, J and Čerņevskis, H and Pētersons, A and Kloviņš, J and Lejnieks, A and Kuzema, V},
title = {Reduced butyrate-producing bacteria and altered metabolic pathways in the gut microbiome of immunoglobulin A nephropathy patients.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28011},
pmid = {40745465},
issn = {2045-2322},
support = {lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/metabolism/pathology ; Female ; *Butyrates/metabolism ; Male ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; *Metabolic Networks and Pathways ; Cross-Sectional Studies ; Feces/microbiology ; *Bacteria/metabolism/genetics/classification ; Prospective Studies ; Immunoglobulin A/metabolism ; Case-Control Studies ; },
abstract = {Gut-associated lymphoid tissue is central to the production of galactose-deficient IgA1 (Gd-IgA1), a key factor in immunoglobulin A nephropathy (IgAN). Although no major differences in gut microbiome diversity have been reported across IgAN cohorts, functional alterations in microbial composition may contribute to disease pathogenesis. The study was designed as a cross-sectional study with an embedded prospective cohort component. Forty-eight adults with biopsy-confirmed IgAN-categorized as progressors (eGFR decline > 5 ml/min/1.73 m[2]/year, n = 23) or nonprogressors (n = 23)-and 23 healthy controls (HC) were recruited. Stool samples underwent metagenomic and functional profiling. Alpha diversity did not differ significantly between IgAN patients and HC. However, butyrate-producing bacteria (Butyrococcus, Agathobacter rectalis) were less abundant in IgAN patients. The sulfoquinovose degradation I pathway, associated with these bacteria, was also reduced. Nucleotide- and nucleoside-biosynthesis pathways were elevated in IgAN. Gd-IgA1 levels correlated with variations in metabolic pathways. Progressors demonstrated enhanced activity in isopropanol biosynthesis, biotin biosynthesis II, and phospholipid biosynthesis pathways. IgAN patients show reduced butyrate-producing bacteria and distinct functional changes in the gut microbiome suggestive of immune activation and inflammation. Progressors exhibit additional metabolic shifts linked to bacterial membrane stabilization.},
}

Humans
*Glomerulonephritis, IGA/microbiology/metabolism/pathology
Female
*Butyrates/metabolism
Male
Adult
*Gastrointestinal Microbiome
Middle Aged
*Metabolic Networks and Pathways
Cross-Sectional Studies
Feces/microbiology
*Bacteria/metabolism/genetics/classification
Prospective Studies
Immunoglobulin A/metabolism
Case-Control Studies

@article {pmid40744923,
year = {2025},
author = {Grossegesse, M and Horn, F and Kurth, A and Lasch, P and Nitsche, A and Doellinger, J},
title = {vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7041},
pmid = {40744923},
issn = {2041-1723},
mesh = {Humans ; *Proteomics/methods ; *SARS-CoV-2/isolation & purification/genetics ; *COVID-19/virology/diagnosis ; *Viruses/genetics/isolation & purification/classification ; Viral Proteins/metabolism ; Workflow ; *Virus Diseases/virology/diagnosis ; Genome, Viral ; Algorithms ; Peptide Library ; Virome ; Sensitivity and Specificity ; Metagenomics/methods ; Nasopharynx/virology ; },
abstract = {Viral infections are commonly diagnosed by the detection of viral genome fragments or proteins using targeted methods such as PCR and immunoassays. In contrast, metagenomics enables the untargeted identification of viral genomes, expanding its applicability across a broader spectrum. In this study, we introduce proteomics as a complementary approach for the untargeted identification of human-pathogenic viruses from patient samples. The viral proteomics workflow (vPro-MS) is based on an in-silico derived peptide library covering the human virome in UniProtKB (331 viruses, 20,386 genomes, 121,977 peptides). A scoring algorithm (vProID score) is developed to assess the confidence of virus identification from proteomics data (https://github.com/RKI-ZBS/vPro-MS). In combination with diaPASEF-based data acquisition, this workflow enables the analysis of up to 60 samples per day. The specificity is determined to be >99,9% in an analysis of 221 plasma, swab and cell culture samples covering 17 different viruses. The sensitivity of this approach for the detection of SARS-CoV-2 in nasopharyngeal swabs corresponds to a PCR cycle threshold of 27 with comparable quantitative accuracy to metagenomics. vPro-MS enables the integration of untargeted virus identification in large-scale proteomic studies of biofluids such as human plasma to detect previously undiscovered virus infections in patient specimens.},
}

Humans
*Proteomics/methods
*SARS-CoV-2/isolation & purification/genetics
*COVID-19/virology/diagnosis
*Viruses/genetics/isolation & purification/classification
Viral Proteins/metabolism
Workflow
*Virus Diseases/virology/diagnosis
Genome, Viral
Algorithms
Peptide Library
Virome
Sensitivity and Specificity
Metagenomics/methods
Nasopharynx/virology

@article {pmid40743118,
year = {2025},
author = {Ozturk, S and Ekmen, FG and Ekmen, H and Ünal, EM and Er, A and Keskin, E and Arbuckle, BS},
title = {Decoding past microbial life and antibiotic resistance in İnonü Cave's archaeological soil.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326358},
pmid = {40743118},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Archaeology ; *Bacteria/genetics/classification/drug effects ; *Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Humans ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Turkey ; },
abstract = {This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.},
}

*Soil Microbiology
*Archaeology
*Bacteria/genetics/classification/drug effects
*Caves/microbiology
RNA, Ribosomal, 16S/genetics
Humans
*Drug Resistance, Microbial/genetics
Microbiota/genetics
Turkey

@article {pmid40742122,
year = {2025},
author = {Wu, H and Jiang, X and Xi, Y and Ning, S and Wu, H and Xin, W and Peng, W and Wang, S and Zhang, W},
title = {Genetic characterization of the marmot gut virome in high-altitude Qinghai Province and identification of novel viruses with zoonotic potential.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0029725},
doi = {10.1128/msphere.00297-25},
pmid = {40742122},
issn = {2379-5042},
abstract = {The high-altitude ecosystems of Qinghai Province, China, harbor unique viral communities shaped by extreme environmental conditions and host adaptations. This study presents a comprehensive genetic characterization of the marmot gut virome, revealing novel viral strains with zoonotic potential. Using viral metagenomics, we analyzed intestinal contents from 70 marmots collected from Chengduo and Maqin counties. Sequencing on the Illumina NovaSeq 6000 platform identified 19 viral genomes belonging to four major families: Adenoviridae, Astroviridae, Parvoviridae, and Picornaviridae, along with four novel circular Rep-encoding single-stranded DNA (CRESS DNA) viruses. Phylogenetic analyses demonstrated close relationships between marmot-derived strains and viruses from humans, bats, and other mammals, highlighting potential cross-species transmission risks. Notably, bat-associated adenoviruses showed closer phylogenetic proximity to human strains, while novel parvoviruses formed a distinct clade within the Dependoparvovirus genus. The discovery of a novel astrovirus with low sequence similarity to known genera underscores the need for taxonomic reclassification. Additionally, a novel picornavirus related to Sapelovirus and four divergent CRESS DNA viruses were identified, expanding our understanding of viral diversity in high-altitude rodents. These findings emphasize the role of marmots as viral reservoirs and highlight the importance of high-altitude ecosystems as hotspots for zoonotic pathogen emergence. This study provides critical insights into viral evolution, host adaptation, and zoonotic risks, advocating for integrated surveillance strategies to mitigate future spillover events.IMPORTANCEViruses are the most abundant and diverse biological entities on Earth, yet their presence in wildlife from extreme environments remains poorly understood. High-altitude ecosystems, shaped by harsh conditions like intense UV radiation and low oxygen levels, create unique settings for virus evolution. This study is the first to comprehensively profile the gut virome of marmots in Qinghai Province, uncovering novel viral strains and highlighting how extreme environments drive viral diversity. Marmots, as key species in these regions, can act as bridges for virus transmission among wildlife, livestock, and humans, posing zoonotic risks. Understanding these viral communities is essential for predicting and preventing future outbreaks. Our findings emphasize the urgent need for integrated, One Health-based surveillance strategies to safeguard both public health and biodiversity in fragile high-altitude ecosystems.},
}

@article {pmid40739184,
year = {2025},
author = {Tang, HB and Si, YX and Li, HD and Dang, W and Lu, HL},
title = {Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {466},
pmid = {40739184},
issn = {1471-2180},
support = {32471577//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Turtles/microbiology ; *Nitrites/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology/veterinary/chemically induced ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Stress, Physiological ; Intestines/microbiology ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; },
abstract = {BACKGROUND: Nitrite is one of the primary pollutants in high-density aquaculture systems, and may cause various toxic effects (e.g., oxidative damage, metabolic and immune dysregulation, histological inflammation, etc.) on economically important aquaculture species, such as echinoderms, crustaceans and fish. Nitrite can also disrupt the intestinal function and microbiota in some fish and amphibians. However, intestinal physiological and microbial responses of cultured turtles under nitrite stress were rarely explored.

METHOD: Twenty Mauremys reevesii juveniles were exposed to different nitrite levels and fed with a commercial diet. Their intestinal content samples were analyzed for microbial diversity and composition.

RESULTS: Nitrite exposure reduced intestinal microbial diversity, with lower α-diversity values in higher-concentration exposed turtles. It also changed the microbial composition. After exposure, the abundances of Bacteroidetes and Firmicutes decreased, but that of Proteobacteria increased at the phylum level. Similarly, abundances of some potentially beneficial bacterial genera, e.g., Prevotella_1, Christensenellaceae_R-7, Muribaculaceae_ge, were shown to decrease, but those of putatively pathogenic genera, e.g., Halomonas, Nesterenkonia, increased at the genus level. Furtherly, potentially altered metabolic pathways (e.g., biosynthesis of ansamycins and vancomycin group antibiotics) were revealed by functional predictions of intestinal microbiota.

CONCLUSION: This study highlighted intestinal microbial dysbiosis and prevalence of putatively pathogenic bacteria in cultured turtles under nitrite stress. Excessive levels of nitrite would alter the health status of aquatic animals by disrupting their intestinal microbiome.},
}

Animals
*Turtles/microbiology
*Nitrites/toxicity
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/microbiology/veterinary/chemically induced
*Bacteria/classification/genetics/drug effects/isolation & purification
Stress, Physiological
Intestines/microbiology
*Water Pollutants, Chemical/toxicity
Aquaculture

@article {pmid40739125,
year = {2025},
author = {Jiang, W and Xiong, M and Feng, S and Liu, Q and Chen, Y and Zou, S and Kang, D},
title = {Water content alters soil organic carbon metabolism via microbial traits in Tibetan alpine peatlands.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27793},
pmid = {40739125},
issn = {2045-2322},
support = {No. 2023NSFSC0143//the Natural Science Foundation of Sichuan Provence/ ; No. 31800458//the National Natural Science Foundation of China/ ; No. 2019-ZL-19//Sichuan Province Transportation Science and Technology Project: Research and Demonstration on Crucial Technologies of Wetland Eco-environment Protection Under the Influence of Highway Engineering on the Western Sichuan Plateau/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; Tibet ; *Water/analysis ; Carbon Cycle ; Archaea/metabolism/genetics ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; Microbiota ; },
abstract = {Alpine peatlands on the eastern Tibetan Plateau are vital carbon sinks, with soil moisture playing a key role in peatland carbon cycling. However, they face disruptions in their carbon balance due to drought, which reduces soil water content. Therefore, this study investigated microbially driven water-carbon interactions through field surveys, laboratory incubations, and metagenomics. Soil drying contributes to changes in both the metabolic quotient (qCO2) and the microbial quotient (Cmic: Corg), as well as the microbial abundance. As the soil water content decreased, both qCO2 and Cmic: Corg exhibited an overall increasing trend. Moreover, soil water content had a more significant effect on soil bacteria, while its effect on fungi and archaea was minimal. Soil microbial carbon decomposition genes were also influenced by changes in soil water content. Next, we used RDA to analyze the relationship between soil respiration quotient values and microbial traits. The results revealed that Actinobacteria were strongly negatively correlated with qCO2, whereas Archaea and Candidatus_R were positively correlated with qCO2. Additionally, Cmic: Corg was closely linked to fungi, and both Proteobacteria and Acidobacteria exhibited positive correlations. qCO2 had a strong negative correlation with genes involved in the degradation of monosaccharides and hemicellulose, whereas Cmic: Corg was positively correlated with genes related to the degradation of cellulose and lignin. Moreover, droughts affected microbial residue carbon and associated carbon metabolic pathways. Therefore, changes in soil water content may be an important factor influencing carbon metabolism processes in peatlands. This study deepens our understanding of the effects of drought on soil metabolism and microbial dynamics in alpine peatlands and provides new insights into the microecological mechanisms of soil carbon cycling in these ecosystems in the context of global change.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism
Tibet
*Water/analysis
Carbon Cycle
Archaea/metabolism/genetics
Bacteria/metabolism/genetics
Fungi/metabolism/genetics
Microbiota

@article {pmid40736894,
year = {2025},
author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK},
title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {71-88},
doi = {10.1007/978-1-0716-4702-8_5},
pmid = {40736894},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; },
abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.},
}

*Metagenomics/methods
*Environmental Monitoring/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Gene Library

@article {pmid40736175,
year = {2025},
author = {Shi, Q and Wei, Z and Pang, J and Qudsi, AI and Wei, M and Zhang, Z and Zhang, Y and Wang, Z and Chen, K and Xu, X and Lu, X and Liang, Q},
title = {Achromobacter in the Conjunctival Sac Microbiota: Potential Association With Acanthamoeba Keratitis Related to Orthokeratology Lenses.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {71},
pmid = {40736175},
issn = {1552-5783},
mesh = {Humans ; Male ; Female ; *Microbiota ; *Acanthamoeba Keratitis/microbiology/etiology ; *Conjunctiva/microbiology ; Adult ; *Achromobacter/isolation & purification/genetics/physiology ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; *Orthokeratologic Procedures/adverse effects/instrumentation ; Acanthamoeba ; *Contact Lenses/adverse effects ; Young Adult ; DNA, Bacterial/genetics/analysis ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {PURPOSE: Acanthamoeba keratitis (AK) is a severe infection linked to orthokeratology lens use, whereas the involvement of conjunctival microbiota in AK remains poorly understood. This study investigates microbiota dysbiosis in AK pathogenesis to inform microbiota-based interventions.

METHODS: Conjunctival swabs from 14 patients with AK and 10 healthy controls underwent 16S rRNA sequencing. Microbiome analysis compared diversity, taxa, and metabolic pathways. Functional assays quantified Achromobacter-enhanced Acanthamoeba adhesion and migration. Metagenomics and fluorescence in situ hybridization (FISH) with species-specific probes confirmed endosymbiosis.

RESULTS: Patients with AK showed reduced bacterial diversity compared with the healthy controls (P < 0.001) but similar richness. Relative abundance of Achromobacter in the AK group was higher compared to the healthy control group (P < 0.001). Achromobacter dominated microbiota among the AK group, being identified as a key biomarker via the linear discriminant analysis effect size (LEfSe). In vitro, Achromobacter increased Acanthamoeba adhesion (P = 0.007) and the migration area (P < 0.05). Metagenomic analysis and FISH further showed Achromobacter spp. as potential endosymbionts of Acanthamoeba. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed upregulated phenylalanine, fatty acid, and propanoate metabolism in the AK group (all P < 0.001). MetaCyc highlighted enriched pyruvate fermentation to isobutanol, aerobic respiration I, and L-isoleucine biosynthesis II in the AK group (P < 0.001).

CONCLUSIONS: AK-associated conjunctival dysbiosis features Achromobacter dominance, reduced diversity, and altered metabolism. Achromobacter is associated with enhanced adhesion and migration of Acanthamoeba, indicating a possible symbiotic interaction and its potential as a biomarker and therapeutic target.},
}

Humans
Male
Female
*Microbiota
*Acanthamoeba Keratitis/microbiology/etiology
*Conjunctiva/microbiology
Adult
*Achromobacter/isolation & purification/genetics/physiology
In Situ Hybridization, Fluorescence
RNA, Ribosomal, 16S/genetics
*Orthokeratologic Procedures/adverse effects/instrumentation
Acanthamoeba
*Contact Lenses/adverse effects
Young Adult
DNA, Bacterial/genetics/analysis
Dysbiosis/microbiology
Middle Aged

@article {pmid40732945,
year = {2025},
author = {Kulecka, M and Jaworski, P and Zeber-Lubecka, N and Bałabas, A and Piątkowska, M and Czarnowski, P and Frączek, B and Tarnowski, W and Mikula, M and Ostrowski, J},
title = {The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
pmid = {40732945},
issn = {2072-6643},
support = {2018/29/B/NZ7/00809//National Science Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Female ; *Metagenomics/methods ; Adult ; Feces/microbiology ; *Dysbiosis/microbiology/diagnosis ; Body Mass Index ; Middle Aged ; Bacteria/classification/genetics ; Workflow ; Case-Control Studies ; Young Adult ; },
abstract = {Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m[2]), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m[2]), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m[2]) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m[2] had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m[2]. Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m[2] obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
Male
Female
*Metagenomics/methods
Adult
Feces/microbiology
*Dysbiosis/microbiology/diagnosis
Body Mass Index
Middle Aged
Bacteria/classification/genetics
Workflow
Case-Control Studies
Young Adult

@article {pmid40731978,
year = {2025},
author = {Garcia, M and Bruna, P and Duran, P and Abanto, M},
title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40731978},
issn = {2076-2607},
abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.},
}

@article {pmid40731321,
year = {2025},
author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M},
title = {The BeeBiome data portal provides easy access to bee microbiome information.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {198},
pmid = {40731321},
issn = {1471-2105},
mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; },
abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.},
}

Bees/microbiology
Animals
*Microbiota/genetics
Metagenomics/methods
*Databases, Genetic
Metagenome

@article {pmid40731267,
year = {2025},
author = {Xu, X and Qin, D and Qin, X and Gao, X and Li, C and Liu, X and Wu, G},
title = {Sustainable management of soil-borne disease: integrating fumigation with Andrographis paniculata residues to rebuild rhizosphere function.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {460},
pmid = {40731267},
issn = {1471-2180},
support = {32060639//the National Natural Science Foundation of China/ ; 202105AC160037, 202205AC160077//the Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Fumigation/methods ; *Andrographis/chemistry ; *Plant Diseases/microbiology/prevention & control ; *Plant Extracts/pharmacology/chemistry ; Metabolomics ; Fusarium/drug effects ; Soil/chemistry ; Microbiota/drug effects ; Metagenomics ; },
abstract = {Continuous pepper cropping induces soil-borne diseases and disrupts rhizosphere microecological balance. This study employed untargeted metabolomics and metagenomics to investigate treatment effects on rhizosphere metabolic reprogramming and microbe-metabolite interactions. Aqueous and ethanolic extracts of Andrographis paniculata residues (TCMR) were rich in flavonoids, terpenoids, and phenolic acids, exhibiting significant inhibition against soil-borne pathogens (Fusarium oxysporum, Fusarium solani, and others; >70% inhibition at high doses). While single fumigation (W1, M1) transiently suppressed pathogens, it disrupted rhizosphere metabolic homeostasis. In contrast, combined fumigation-TCMR treatments (WC, MC) enhanced plant stress resistance, stabilized membrane integrity, and reshaped microbial communities by modulating amino acid, lipid, and phenylpropanoid biosynthesis pathways. Microbe-metabolite network analysis revealed that coupling carbon-nitrogen cycling with redox homeostasis drives soil microecological optimization. This integrated strategy provides a sustainable solution for continuous cropping obstacles through synergistic metabolic reprogramming and microbiome reconstruction.},
}

*Rhizosphere
*Soil Microbiology
*Fumigation/methods
*Andrographis/chemistry
*Plant Diseases/microbiology/prevention & control
*Plant Extracts/pharmacology/chemistry
Metabolomics
Fusarium/drug effects
Soil/chemistry
Microbiota/drug effects
Metagenomics

@article {pmid40730965,
year = {2025},
author = {Clark-Boucher, D and Coull, BA and Reeder, HT and Wang, F and Sun, Q and Starr, JR and Lee, KH},
title = {Group-wise normalization in differential abundance analysis of microbiome samples.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {196},
pmid = {40730965},
issn = {1471-2105},
support = {U01 HD052104/HD/NICHD NIH HHS/United States ; T32 GM135117/GM/NIGMS NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; T32GM135117/GM/NIGMS NIH HHS/United States ; R03 DE027486/DE/NIDCR NIH HHS/United States ; P30ES000002/ES/NIEHS NIH HHS/United States ; R01 GM126257/GM/NIGMS NIH HHS/United States ; U01 HD052102/HD/NICHD NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; P01 HD103133/HD/NICHD NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; Metagenome ; Algorithms ; *Metagenomics/methods ; Humans ; },
abstract = {BACKGROUND: A key challenge in differential abundance analysis (DAA) of microbial sequencing data is that the counts for each sample are compositional, resulting in potentially biased comparisons of the absolute abundance across study groups. Normalization-based DAA methods rely on external normalization factors that account for compositionality by standardizing the counts onto a common numerical scale. However, existing normalization methods have struggled to maintain the false discovery rate in settings where the variance or compositional bias is large. This article proposes a novel framework for normalization that can reduce bias in DAA by re-conceptualizing normalization as a group-level task. We present two new normalization methods within the group-wise framework: group-wise relative log expression (G-RLE) and fold-truncated sum scaling (FTSS).

RESULTS: G-RLE and FTSS achieve higher statistical power for identifying differentially abundant taxa than existing methods in model-based and synthetic data simulation settings. The two novel methods also maintain the false discovery rate in challenging scenarios where existing methods suffer. The best results are obtained from using FTSS normalization with the DAA method MetagenomeSeq.

CONCLUSION: Compared with other methods for normalizing compositional sequence count data prior to DAA, the proposed group-level normalization frameworks offer more robust statistical inference. With a solid mathematical foundation, validated performance in numerical studies, and publicly available software, these new methods can help improve rigor and reproducibility in microbiome research.},
}

*Microbiota/genetics
Metagenome
Algorithms
*Metagenomics/methods
Humans

@article {pmid40730483,
year = {2025},
author = {Zhong, H and Song, Y and Hu, S and Zhang, C and Li, L},
title = {Metagenomics-Metabolomics Reveals the Alleviation of Indole-3-Ethanol on Radiation-Induced Enteritis in Mice.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2502037},
pmid = {40730483},
issn = {1738-8872},
mesh = {Animals ; *Indoles/pharmacology/metabolism ; *Enteritis/drug therapy/etiology/metabolism/microbiology/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Anti-Inflammatory Agents/pharmacology ; Colon/pathology/drug effects/radiation effects ; Cytokines/metabolism ; Interleukin-17/metabolism ; },
abstract = {Indole-3-ethanol (IEt), a small molecule metabolite from intestinal microbial tryptophan metabolism, has been established to have anti-inflammatory properties. However, its effect on radiation-induced enteritis has not been reported. Here, we aim to explore the effects and potential mechanisms of IEt on radiation enteritis. C57BL/6J mice were orally administered an IEt solution before radiation exposure. Inflammatory factors, including IL-17A, IFN-γ, IL-6 and IL-1β, were detected using enzyme-linked immunosorbent assay. Colonic histopathology was assessed through H&E staining. Subsequently, gut microbiota and its metabolites were analyzed using metagenomics and metabolomics. The results suggested that IEt alleviated radiation-induced enteritis, as evidenced by improved colonic structural integrity, decreased levels of pro-inflammatory factors like IL-17A, and the restoration of intestinal microecological and metabolic balance. IEt enriched the abundance of Lachnospiraceae family members, particularly the genus Roseburia - a known anti-inflammatory commensal. In addition, IEt upregulated the levels of metabolites with anti-inflammatory effects such as indole-3-carbinol, pteridine, and pyropheophorbide-a. Furthermore, Roseburia was significantly positively correlated with indole-3-carbinol and negatively correlated with the pro-inflammatory factor IL-17A. Therefore, IEt may alleviate radiation enteritis through Roseburia-indole-3-carbinol and Roseburia-IL-17A axes. This study revealed the potential mechanisms by which IEt alleviated radiation enteritis, providing a potential protective candidate for radiation enteritis.},
}

Animals
*Indoles/pharmacology/metabolism
*Enteritis/drug therapy/etiology/metabolism/microbiology/pathology
Mice
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Metabolomics/methods
*Metagenomics/methods
Male
*Anti-Inflammatory Agents/pharmacology
Colon/pathology/drug effects/radiation effects
Cytokines/metabolism
Interleukin-17/metabolism

@article {pmid40728669,
year = {2025},
author = {Priyadarsini, M and Dhoble, AS},
title = {Combination of flow cytometry and metagenomics to monitor the effect of raw vs digested manure on microbial diversity in anaerobic digestion of Napier grass.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {8},
pages = {963},
pmid = {40728669},
issn = {1573-2959},
support = {SPARC/2019-2020/P1570/SL//Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; },
mesh = {*Manure/microbiology ; Flow Cytometry ; Metagenomics ; *Poaceae/microbiology ; Anaerobiosis ; *Microbiota ; Biofuels ; Bacteria ; Archaea ; Animals ; },
abstract = {Microbiomes play a crucial role in anaerobic digestion (AD), by degrading the complex lignocellulosic biomass leading to biomethane production. This study emphasizes the role of microbial diversity and its impact on the digester's performance with raw (CD) and digested manure (ADS) as a source of microbiome and Napier grass (NG) as feedstock. The integration of flow cytometry and metagenomics provides a novel perspective on microbial dynamics during anaerobic digestion. Initially, the inocula (ADS and CD) had 354 bacterial and 8 archaeal genera in common that decreased to 39 bacteria and 1 archaeon at the end of experiment, indicating significant shift in microbial diversity during the process. Metagenome sequencing showed that Clostridium was the most abundant genera in NG digested with ADS, while Prevotella was in NG digested with CD. An approximately 2.45% increase in Clostridium in NG digested with ADS led to VFA accumulation and pH drop, inhibiting methanogens and lower biogas production. Most of the flow cytometric populations showed positive correlation with Prevotella suggesting its key role in breaking down of complex substrate. The population 2, 3, and 5 positively correlated to biogas production. NG digested with CD produced nearly twice biogas yield (1064.33 ± 119.97 mL) compared to ADS (508 ± 20.95 mL) which corresponds to the enhanced microbial activity in CD. These findings suggest that microbiome of CD might be better acclimatized for NG degradation than ADS as NG is often used as cattle fodder.},
}

*Manure/microbiology
Flow Cytometry
Metagenomics
*Poaceae/microbiology
Anaerobiosis
*Microbiota
Biofuels
Bacteria
Archaea
Animals

@article {pmid40728577,
year = {2025},
author = {Raziq, MF and Manzoor, H and Kayani, MUR},
title = {Non-small Cell Lung Cancer, Immunotherapy and the Influence of Gut Microbiome.},
journal = {Current microbiology},
volume = {82},
number = {9},
pages = {419},
pmid = {40728577},
issn = {1432-0991},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology ; *Immunotherapy/methods ; *Lung Neoplasms/therapy/microbiology/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {Lung cancer remains the second most commonly diagnosed cancer and the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC), accounting for approximately 85% of lung cancer cases, is the most prevalent form. Treatment options for NSCLC include surgery, radiation therapy, chemotherapy, immunotherapy, and targeted drug therapies. Among these, immune checkpoint inhibitors targeting PD-1/PD-L1 have demonstrated significant potential, particularly in improving treatment outcomes. However, their clinical efficacy is impeded by challenges such as toxicity, resistance development, and variable patient responses. Emerging evidence highlights the critical role of the gut microbiome as an important modulator of immune responses in NSCLC, particularly in the context of anti-PD-1/PD-L1 therapies. Specific gut microbes, such as Akkermansia muciniphila, have been associated with improved responses to immunotherapy, suggesting that modulation of the gut microbiome may enhance treatment outcomes. This review discusses the current understanding of the influence of gut microbiome on NSCLC and its potential to improve the clinical efficacy of anti-PD-1/PD-L1 therapies. By integrating microbiome-based insights into personalized treatment strategies, we can overcome the limitations of current immunotherapy approaches and optimize patient outcomes. This review aims to serve as a resource for the scientific community by providing insights into how modulation of gut microbiome may enhance treatment outcomes in NSCLC patients receiving anti-PD-1/PD-L1 immunotherapy.},
}

Humans
*Gastrointestinal Microbiome
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology
*Immunotherapy/methods
*Lung Neoplasms/therapy/microbiology/immunology
Immune Checkpoint Inhibitors/therapeutic use
Animals

@article {pmid40726156,
year = {2025},
author = {Yang, S and Huang, X and Li, X and Feng, J and Chen, P and Cao, Z and He, L and Li, C and Li, Z and Xie, M},
title = {Aloe vera polysaccharides mitigate high-fat high-cholesterol diet-induced atherosclerosis in ApoE[-/-] mice via regulation of lipid metabolism and gut microbiota.},
journal = {Food & function},
volume = {16},
number = {16},
pages = {6671-6686},
doi = {10.1039/d5fo01995h},
pmid = {40726156},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Atherosclerosis/drug therapy/metabolism/etiology ; Diet, High-Fat/adverse effects ; Mice ; *Lipid Metabolism/drug effects ; *Aloe/chemistry ; Male ; *Polysaccharides/pharmacology/administration & dosage ; Apolipoproteins E/genetics ; Mice, Inbred C57BL ; RAW 264.7 Cells ; Disease Models, Animal ; },
abstract = {Cardiovascular diseases are leading causes of death globally, often manifesting after years of atherosclerosis (AS) progression. In this study, we investigated the atheroprotective effects of three different sources of glucomannan, Dendrobium officinale polysaccharide, Konjac glucomannan, and Aloe vera polysaccharide (AVP), using an in vitro ox-LDL-induced foam cell model and an in vivo high-fat high-cholesterol diet-fed ApoE[-/-] mouse model. Both settings indicate that AVP exerts the most significant atheroprotective effects. It inhibits lipid absorption and enhances the regulation of lipid homeostasis by the liver X receptor, thereby suppressing the formation of foam cells. It can also alleviate ox-LDL-induced oxidative stress and apoptosis in RAW 264.7 cells. Animal experiments show that AVP can prevent the formation of atherosclerotic plaques and coronary artery fibrosis, while also reducing circulating IL-1β levels. Furthermore, liver transcriptomic analysis shows that AVP inhibits inflammation and promotes bile acid excretion and transport by upregulating the farnesoid X receptor. Additionally, metagenomic analysis indicates that AVP can significantly reverse the microbial alterations associated with AS. Specific gut microbes, such as Prevotella, may partially mediate the effects of AVP through the gut-liver axis. This is the first study to report the atheroprotective effects of AVP, demonstrating that it alleviates atherosclerosis by restoring lipid metabolism homeostasis and modulating the gut microbiome.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Atherosclerosis/drug therapy/metabolism/etiology
Diet, High-Fat/adverse effects
Mice
*Lipid Metabolism/drug effects
*Aloe/chemistry
Male
*Polysaccharides/pharmacology/administration & dosage
Apolipoproteins E/genetics
Mice, Inbred C57BL
RAW 264.7 Cells
Disease Models, Animal

@article {pmid40724992,
year = {2025},
author = {Rušanac, A and Škibola, Z and Matijašić, M and Čipčić Paljetak, H and Perić, M},
title = {Microbiome-Based Products: Therapeutic Potential for Inflammatory Skin Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40724992},
issn = {1422-0067},
support = {NPOO.C3.2.R3-I1.04.0240//European Regional Development Fund/ ; KK.01.2.1.02.0137//European Regional Development Fund/ ; IP.1.1.03.0157//European Regional Development Fund/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; *Skin Diseases/microbiology/therapy ; Dysbiosis/microbiology/therapy ; Skin/microbiology ; Animals ; Psoriasis/microbiology/therapy ; Dermatitis, Atopic/microbiology/therapy ; },
abstract = {Maintaining a balanced skin microbiota is essential for skin health, whereas disruptions in skin microbiota composition, known as dysbiosis, can contribute to the onset and progression of various skin disorders. Microbiota dysbiosis has been associated with several inflammatory skin conditions, including atopic dermatitis, seborrheic dermatitis, acne, psoriasis, and rosacea. Recent advances in high-throughput sequencing and metagenomic analyses have provided a deeper understanding of the skin microbial communities in both health and disease. These discoveries are now being translated into novel therapeutic approaches aimed at restoring microbial balance and promoting skin health through microbiome-based interventions. Unlike conventional therapies that often disrupt the microbiota and lead to side effects or resistance, microbiome-based products offer a more targeted strategy for preventing and managing inflammatory skin diseases. These products, which include probiotics, prebiotics, postbiotics, and live biotherapeutic agents, are designed to modulate the skin ecosystem by enhancing beneficial microbial populations, suppressing pathogenic strains, and enhancing immune tolerance. As a result, they represent a promising class of products with the potential to prevent, manage, and even reverse inflammatory skin conditions. However, realizing the full therapeutic potential of microbiome-based strategies in dermatology will require continued research, robust clinical validation, and clear regulatory frameworks.},
}

Humans
*Microbiota/drug effects
Probiotics/therapeutic use
Prebiotics/administration & dosage
*Skin Diseases/microbiology/therapy
Dysbiosis/microbiology/therapy
Skin/microbiology
Animals
Psoriasis/microbiology/therapy
Dermatitis, Atopic/microbiology/therapy

@article {pmid40723458,
year = {2025},
author = {Penalba-Iglesias, D and Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Probanza, A and Jiménez-Gómez, PA},
title = {Use of Bacillus pretiosus and Pseudomonas agronomica for the Synthesis of a Valorized Water Waste Treatment Plant Waste as a Biofertilizer Intended for Quercus pyrenaica L. Fertigation.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723458},
issn = {2079-7737},
support = {TED2021-132285A-I00//Next Generation Funds/ ; },
abstract = {The loss of hectares of forest areas has become a global issue that has worsened over recent years due to unsustainable human activities. In a context of limited availability of productive land, it is urgent to adopt efficient strategies to recover the affected natural areas. Actions based on a circular economy, such as the use of organic chemical matrices recovered from water waste treatment plant waste, have proven to be effective. In this regard, the addition of plant growth-promoting bacteria (PGPB), such as Bacillus pretiosus and Pseudomonas agronomica, can contribute to the chemical treatment, favoring the recovery of soils, accelerating the recovery of vegetation cover, and inducing an increase in biodiversity. In this research, the effect of bio-fertigation under controlled laboratory conditions in Quercus pyrenaica is evaluated. After a thirty-six-week trial, the biometric and nutritional parameters of the plants were harvested and measured, and the diversity and composition of the metagenomes of their rhizospheres were evaluated. As well, the cenoantibiogram and the metabolic diversity were measured. The results showed that the use of these biofertilizers increased the variables related to plant production, quality of plant composition as an indirect means of their resilience, as well as an increase in rhizospheric microbial diversity and a reduction in their MIC resistance to the most widely used antibiotics. For all these reasons, the use of the biofertilizer result of the combination of WWTP waste, Bacillus pretiosus, and Pseudomonas agronomica is postulated as an environmentally friendly strategy that can contribute to the recovery of potential oak forest areas.},
}

@article {pmid40721426,
year = {2025},
author = {Yang, Y and Ye, M and Song, Y and Xing, W and Zhao, X and Li, Y and Shen, J and Zhou, J and Arikawa, K and Wu, S and Song, Y and Xu, N},
title = {Gut microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {146},
pmid = {40721426},
issn = {2055-5008},
support = {2020YFC2003700//National Key R&D Plan/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 20Z11901000, 20DZ2261200, 20XD1401200, 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; SHDC2020CR5010-002//Clinical Research Plan of SHDC/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; ZY(2021-2023)-0207-01//Shanghai Municipal Health Commission and Shanghai Municipal Administrator of Traditional Chinese Medicine/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy ; *Immunotherapy/methods ; Animals ; *Lung Neoplasms/therapy/microbiology/drug therapy ; Mice ; *Fatty Acids, Volatile/metabolism ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Male ; Metagenomics ; Middle Aged ; Aged ; Dysbiosis/microbiology ; Antineoplastic Agents/therapeutic use ; },
abstract = {The role of gut dysbiosis in shaping immunotherapy responses is well-recognized, yet its effect on the therapeutic efficacy of chemotherapy and immunotherapy combinations remains poorly understood. We analyzed gut microbiota in non-small cell lung cancer (NSCLC) patients treated with chemo-immunotherapy, comparing responders and non-responders using 16S rRNA sequencing. Responders showed higher microbial richness and abundance of specific genera like Faecalibacterium and Subdoligranulum, and the phylum Firmicutes. Support vector machine (SVM), a machine learning model based on microbial composition, predicted treatment efficacy with the area under the curve (AUC) values of 0.763 for genera and 0.855 for species. Metagenomic analysis revealed significant differences in metabolic pathways, with responders exhibiting higher short-chain fatty acids (SCFAs) production. Fecal microbiota transplantation (FMT) and SCFAs supplementation in mouse models enhanced treatment efficacy by promoting effector T cell activity in tumors. Our study suggests that gut microbiota, through SCFAs production, regulates chemo-immunotherapy efficacy, offering new strategies to improve NSCLC treatment outcomes.},
}

*Gastrointestinal Microbiome
Humans
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy
*Immunotherapy/methods
Animals
*Lung Neoplasms/therapy/microbiology/drug therapy
Mice
*Fatty Acids, Volatile/metabolism
Fecal Microbiota Transplantation
RNA, Ribosomal, 16S/genetics
Treatment Outcome
*Bacteria/classification/genetics/isolation & purification/metabolism
Female
Male
Metagenomics
Middle Aged
Aged
Dysbiosis/microbiology
Antineoplastic Agents/therapeutic use

@article {pmid40716139,
year = {2025},
author = {Lemos-Lucumi, CA and Cárdenas-Hernández, V and Toro-Perea, N},
title = {Metagenomic and metatranscriptomic exploration of Avicennia germinans L.: Endophytic microbiome of leaves and roots.},
journal = {Microbiological research},
volume = {300},
number = {},
pages = {128287},
doi = {10.1016/j.micres.2025.128287},
pmid = {40716139},
issn = {1618-0623},
mesh = {*Endophytes/genetics/classification/isolation & purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Avicennia/microbiology ; *Microbiota ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Gene Expression Profiling ; Transcriptome ; Metagenome ; },
abstract = {Mangroves are productive coastal ecosystems with extreme environmental conditions of temperature, salinity and anthropogenic pollution. Their associated microbiota plays an essential role in plant survival, yet their functional dynamics remain poorly understood. This study characterizes the endophytic microbiome of Avicennia germinans L. in the Buenaventura Bay mangrove ecosystem (Colombia), using a combined metagenomic and metatranscriptomic approach. Distinct microbial communities were observed in leaves and pneumatophores. Root-associated endophytes exhibited higher taxonomic richness and greater transcriptional activity. Functional gene expression revealed enrichment of pathways related to osmotic and oxidative stress responses, hydrocarbon degradation, nitrogen metabolism, and ion homeostasis. The expression of efflux pumps, NADH dehydrogenase, cytochromes, chaperones, H[+]-ATPases, and H[+]/Na[+] antiporters suggest active microbial participation in salinity, heavy metal, xenobiotics and stress resistance. These findings highlight the adaptive versatility of the endophytic microbiome in A. germinans and support its potential for biotechnological applications in stress resistance and bioremediation.},
}

*Endophytes/genetics/classification/isolation & purification
*Plant Roots/microbiology
*Plant Leaves/microbiology
*Avicennia/microbiology
*Microbiota
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Gene Expression Profiling
Transcriptome
Metagenome

@article {pmid40720840,
year = {2025},
author = {Slizovskiy, IB and Gaire, TN and Ferm, PM and Odland, CA and Dee, SA and Nerem, J and Bravo, JE and Kimball, AD and Boucher, C and Noyes, NR},
title = {Reducing skin microbiome exposure impacts through swine farm biosecurity.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf062},
pmid = {40720840},
issn = {2047-217X},
support = {/NH/NIH HHS/United States ; 1R01AI141810-01//National Institute of Allergy and Infectious Diseases/ ; 5U54OH010170-13A/OH/NIOSH CDC HHS/United States ; },
mesh = {*Microbiota ; *Skin/microbiology ; Animals ; Swine/microbiology ; Humans ; Farms ; *Biosecurity ; *Occupational Exposure ; Female ; Male ; Adult ; Bacteria/genetics/classification/isolation & purification ; Longitudinal Studies ; Animal Husbandry ; Skin Microbiome ; },
abstract = {BACKGROUND: Livestock work is unique due to worker exposure to animal-associated microbiomes within the workplace. Swine workers are a unique cohort within the US livestock labor force, as they have direct daily contact with pigs and undertake mandatory biosecurity interventions. However, investigating this occupational cohort is challenging, particularly within tightly regulated commercial swine operations. Thus, little is known about the impacts of animal exposure and biosecurity protocols on the swine worker microbiome. We obtained unique samples from US swine workers, using a longitudinal study design to investigate temporal microbiome dynamics.

RESULTS: We observed a significant increase in bacterial DNA load on worker skin during the workday, with concurrent changes in the composition and abundance of microbial taxa, resistance genes, and mobile genetic elements. However, mandatory showering at the end of the workday partially returned the skin's microbiome and resistome to their original state.

CONCLUSIONS: These novel results from a human cohort demonstrate that existing biosecurity practices can ameliorate work-associated microbiome impacts.},
}

*Microbiota
*Skin/microbiology
Animals
Swine/microbiology
Humans
Farms
*Biosecurity
*Occupational Exposure
Female
Male
Adult
Bacteria/genetics/classification/isolation & purification
Longitudinal Studies
Animal Husbandry
Skin Microbiome

@article {pmid40719990,
year = {2025},
author = {Naqvi, SAH and Umar, UUD and Rehman, AU},
title = {Beneficial communities from core bacterial microbiota of Oryza sativa L. soil and leaves perform dynamic role in growth promotion and suppression of bacterial leaf blight.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {285},
pmid = {40719990},
issn = {1573-0972},
mesh = {*Oryza/microbiology/growth & development ; *Soil Microbiology ; *Plant Leaves/microbiology/growth & development ; Xanthomonas/pathogenicity/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Plant Diseases/microbiology/prevention & control ; *Microbiota/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Pakistan ; Biological Control Agents ; Soil/chemistry ; Metagenomics ; Phylogeny ; },
abstract = {Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), severely threatens global rice production, highlighting the urgent need for sustainable alternatives to chemical pesticides. This study investigates the rhizosphere and phyllosphere microbiomes of Oryza sativa in Punjab, Pakistan, to identify native biocontrol agents (BCAs) with potential to suppress BLB. Using 16S rRNA amplicon sequencing (V3-V9 regions), we analyzed soil and leaf samples from 10 agricultural districts. Microbial diversity, community structure, and functional potential were assessed via bioinformatics tools (QIIME 2, DADA2, PICRUSt2), with a focus on taxa antagonistic to Xoo. Healthy rhizospheres exhibited significantly higher alpha diversity (Shannon index: 6.8 vs. 4.2 in leaves; *p* < 0.001), dominated by copiotrophic taxa (Proteobacteria, Bacteroidetes) linked to organic inputs and root exudates. Diseased soils favored oligotrophic Actinobacteria and Chloroflexi. Functional metagenomics revealed enrichment of siderophore biosynthesis, antibiotic production, and nutrient-cycling genes in healthy soils. Antagonistic genera (Bacillus, Pseudomonas, Streptomyces) demonstrated chitinase and surfactin activity against Xoo, while diseased samples showed elevated Xanthomonas and Erwinia abundances correlating with BLB severity. Native BCAs outperformed non-native strains in colonization and nutrient competition, highlighting their adaptability to local agroecological conditions. Our findings position native BCAs as pivotal tools for BLB suppression and sustainable agriculture, reducing reliance on synthetic chemicals. Field trials confirmed that microbial consortia formulations reduced BLB incidence by 40% and increased yield by 18%. These findings highlight the potential of microbiome-driven strategies to mitigate BLB, reduce chemical reliance, and foster sustainable agricultural practices. Future work should integrate multi-omics approaches to optimize microbial solutions for climate resilience and scale their adoption through policy frameworks.},
}

*Oryza/microbiology/growth & development
*Soil Microbiology
*Plant Leaves/microbiology/growth & development
Xanthomonas/pathogenicity/growth & development
*Bacteria/classification/genetics/isolation & purification
*Plant Diseases/microbiology/prevention & control
*Microbiota/genetics
Rhizosphere
RNA, Ribosomal, 16S/genetics
Pakistan
Biological Control Agents
Soil/chemistry
Metagenomics
Phylogeny

@article {pmid40719366,
year = {2025},
author = {Wang, X and Wang, N and Gao, T and Zhang, Y and Fu, Z and Zhao, Y and Huang, Y and Zheng, X and Gao, X and Lu, L and Yang, L},
title = {Symptom-specific gut microbial and metabolic profiles in ADHD reveal SCFA deficiency as a Key pathogenic mechanism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2537755},
pmid = {40719366},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; *Attention Deficit Disorder with Hyperactivity/microbiology/metabolism ; Animals ; Humans ; Mice ; Male ; Female ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Fecal Microbiota Transplantation ; Child ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metabolome ; Adolescent ; Metabolomics ; },
abstract = {Previous evidence links gut microbiota to attention-deficit/hyperactivity disorder (ADHD) through the gut-brain axis. However, the specific microbiota contributing to symptoms remain unclear. To characterize the gut microbial profile related to different symptoms and explore the mediation mechanism between microbiota alterations and the core ADHD symptoms, we conducted shotgun metagenomic sequencing and fecal metabolomics analysis on 94 ADHD patients and 94 age- and gender-matched controls. Microbial characteristics of three subgroups exhibiting different ADHD core symptom presentations were analyzed. We developed a metabolic model and conducted causal mediation analyses to examine how metabolites connect the microbiota to the symptoms. Fecal microbiota transplantation in mice was employed to validate the findings. The redundancy analysis identified ADHD symptoms as environmental gradients and explained the changes in beta diversity (F = 1.345, pFDR = 0.015). Greater gut microbial alterations were observed in combined presentations (ADHD-C). Several beneficial bacteria involved in short-chain fatty acid synthesis were found to be downregulated, with Lactobacillus sanfranciscensis notably linked to all three core symptoms (p.adj = 1.04E-13; p.adj = 5.07E-07; p.adj = 2.61E-05). Various taxa, functional pathways, and metabolites associated with specific ADHD symptom domains were identified. Imidazoleacetic acid partially mediated the effects between Lactobacillus sanfranciscensis and inattention (p = 0.012). In mice subjected to feces from ADHD patients with a low abundance of Lactobacillus sanfranciscensis, treatment with this strain greatly improved both hyperactivity (t = 2.665, p = 0.0237) and inattention (t = 2.389, p = 0.0380), while acetate supplementation only alleviated inattention (t = 2.362, p = 0.0398). Our findings suggest that different ADHD symptoms were related to common and different gut microbiota and metabolites. Fecal microbiota transplantation in mice validated the hypothesis that gut microbial composition affects ADHD symptoms through metabolic alterations. This study provides more insight into the mechanisms underlying metabolic disturbances in ADHD and elucidates the role of gut microbiota in these processes.},
}

*Gastrointestinal Microbiome/physiology
*Attention Deficit Disorder with Hyperactivity/microbiology/metabolism
Animals
Humans
Mice
Male
Female
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Fecal Microbiota Transplantation
Child
*Bacteria/classification/metabolism/genetics/isolation & purification
Metabolome
Adolescent
Metabolomics

@article {pmid40715283,
year = {2025},
author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM},
title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27297},
pmid = {40715283},
issn = {2045-2322},
mesh = {*Biofilms/growth & development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; },
abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.},
}

*Biofilms/growth & development
*Hot Springs/microbiology
*Metagenome
Hot Temperature
*Bacteria/genetics/metabolism/classification
Microbiota
Phylogeny
Biodiversity
Genome, Bacterial
Metagenomics/methods
Malaysia

@article {pmid40715043,
year = {2025},
author = {Duchesneau, K and Aldeguer-Riquelme, B and Petro, C and Makke, G and Green, M and Tfaily, M and Wilson, R and Roth, SW and Johnston, ER and Kluber, LA and Schadt, CW and Trejo, JB and Callister, SJ and Purvine, SO and Chanton, JP and Hanson, PJ and Tringe, S and Eloe-Fadrosh, E and Glavina Del Rio, T and Konstantinidis, KT and Kostka, JE},
title = {Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6869},
pmid = {40715043},
issn = {2041-1723},
support = {DE-SC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Microbiota/genetics/physiology ; Methane/metabolism ; Metagenome ; Carbon/metabolism ; Climate Change ; Bacteria/metabolism/genetics/classification ; Global Warming ; Ecosystem ; Electrons ; },
abstract = {The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.},
}

*Soil Microbiology
*Soil/chemistry
*Microbiota/genetics/physiology
Methane/metabolism
Metagenome
Carbon/metabolism
Climate Change
Bacteria/metabolism/genetics/classification
Global Warming
Ecosystem
Electrons

@article {pmid40714398,
year = {2025},
author = {Wu, L and Yan, M and Huang, X and Liao, H and Bao, D and Ge, Y and Wang, S and Xia, X},
title = {Temperature-mediated shift from competitive to facilitative interactions between lactic acid bacteria and bacillus species in daqu fermentation: Insights from metagenomics, dual RNA-seq, and coculture analysis.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111352},
doi = {10.1016/j.ijfoodmicro.2025.111352},
pmid = {40714398},
issn = {1879-3460},
abstract = {Daqu, a pivotal starter that defines the flavor profile and quality of Baijiu, undergoes dynamic temperature changes during its production, significantly influencing the microbial community structure and function. Although the importance of fermentation temperature in shaping microbial biodiversity is well-recognized, its impact on microbial interaction dynamics and the underlying mechanisms remains poorly understood. This study integrates metagenomics, dual RNA-seq, and coculture experiments to elucidate temperature-dependent microbial interactions during Daqu fermentation. Metagenomic analysis revealed that lactic acid bacteria (LAB) and Bacillus are dominant genera with distinct thermal preferences that nevertheless coexist throughout the fermentation process. Elevated temperature stress was found to enhance positive microbial interactions within the Daqu ecosystem. Dual RNA-seq analysis uncovered temperature-responsive gene expression patterns associated with oxidative stress, metabolic capacity, and environmental information processing in representative LAB and Bacillus strains. Guided by these multi-omics findings, co-culture assays demonstrated a temperature-dependent shift in microbial interaction modes. At 30 °C, Lactococcus lactis secretes lactic acid that inhibits the growth of Bacillus subtilis, whereas at 50 °C, B. subtilis alleviates oxidative stress in L. lactis by producing cobalamin, thereby enabling short-term rescue and sustained coexistence over serial transfers. These findings provide critical insights into the temperature-driven modulation of microbial interactions, enhancing the precision and manageability of the Daqu fermentation process.},
}

@article {pmid40713905,
year = {2025},
author = {Zhou, J and Zhang, CJ and Zou, D and Gu, C and Li, M},
title = {Magnetite drives microbial community restructuring and stimulates aceticlastic methanogenesis of type II Methanosarcina in mangrove sediments.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {174},
pmid = {40713905},
issn = {2049-2618},
support = {42207144//National Natural Science Foundation of China/ ; 32225003, 32393971, and 32393970//National Natural Science Foundation of China/ ; 2024A1515010843//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; KCXFZ20240903092800002//Shenzhen Science and Technology Program/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; },
mesh = {*Methane/metabolism/biosynthesis ; *Ferrosoferric Oxide/pharmacology/metabolism ; *Geologic Sediments/microbiology ; Wetlands ; *Methanosarcina/metabolism/genetics/classification/isolation & purification/drug effects ; *Microbial Consortia/drug effects ; *Microbiota/drug effects ; Acetates/metabolism ; Lactic Acid/metabolism ; },
abstract = {BACKGROUND: Mangrove wetlands are critical hotspots of methane emissions, yet the role of naturally occurring minerals in shaping their microbial communities and methanogenic processes is poorly understood. Magnetite, a common iron mineral in soils and sediments, has been reported to enhance aceticlastic methanogenesis and facilitate syntrophic methanogenesis. In this study, we integrated multi-omic profiling with cultivation-based approaches to investigate the impact of magnetite on methanogenesis of microbial consortia derived from mangrove sediments, using lactate as a substrate.

RESULTS: Across five serial transfers, mangrove microbial consortia converted lactate to propionate and acetate, which were subsequently degraded into methane. Magnetite addition significantly stimulated methane production, leading to notable changes in community structure, particularly for aceticlastic methanogens, with Methanosarcina predominating in the magnetite-amended cultures and Methanothrix in controls. Four Methanosarcina strains T3, T4, T13, and MeOH were subsequently isolated from magnetite-amended cultures. Combined analyses of metagenome-assembled genomes and the genomes of these isolates revealed that the enriched Methanosarcina in magnetite-amended cultures belonged to type II deficient in hydrogenotrophic methanogenesis pathway. Metatranscriptomic analyses suggested that magnetite addition stimulated aceticlastic methanogenesis of type II Methanosarcina and hydrogenotrophic methanogenesis of Methanomicrobiales in the consortia. Furthermore, pure culture experiments confirmed that magnetite stimulated aceticlastic methanogenesis by Methanosarcina sp. T3, although its gene expression patterns differed from those observed in the microbial consortia. Additionally, Methanofastidiosales, an uncultured archaeal lineage possessing H2-dependent methylotrophic methanogenesis, was detected in all transfers.

CONCLUSIONS: Our findings demonstrate that magnetite alters methanogenic consortia in mangrove sediments, selectively stimulating aceticlastic methanogenesis of type II Methanosarcina and modulating hydrogenotrophic activity in Methanomicrobiales. By integrating multi-omics analyses with pure culture validation, we demonstrate, for the first time, that magnetite directly enhances the aceticlastic methanogenesis of type II non-hydrogenotrophic Methanosarcina. This study provides new insights into the influence of magnetite on complex microbial consortia, offers a deeper understanding of the physiology of type II non-hydrogenotrophic Methanosarcina, and advances knowledge of mineral-mediated regulation of methanogenic networks in anoxic environments. Video Abstract.},
}

*Methane/metabolism/biosynthesis
*Ferrosoferric Oxide/pharmacology/metabolism
*Geologic Sediments/microbiology
Wetlands
*Methanosarcina/metabolism/genetics/classification/isolation & purification/drug effects
*Microbial Consortia/drug effects
*Microbiota/drug effects
Acetates/metabolism
Lactic Acid/metabolism

@article {pmid40713701,
year = {2025},
author = {Bhardwaj, K and Niharika, and Garg, A and Jain, A and Kumar, M and Datt, M and Singh, V and Vrati, S},
title = {Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {254},
pmid = {40713701},
issn = {1743-422X},
support = {BT/PR18657/BIC/101/507/2016//Department of Biotechnology, Ministry of Science and Technology, India/ ; JCB/2021/000015//Science and Engineering Research Board/ ; },
mesh = {Humans ; *Genome, Viral ; *Metagenome ; Feces/virology ; *Virome ; Metagenomics ; *Gastrointestinal Tract/virology ; *Viruses/genetics/classification/isolation & purification ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Metagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains uncharacterized. In this study, we mined a collection of 1090 metagenome assembled "high quality" viral genomes (> 90% completeness, as determined by CheckV) derived from human fecal samples. Sequence analysis revealed eight new species spanning seven genera within the class, Caudoviricetes and nineteen new species from fourteen genera within the ssDNA virus family, Microviridae. Additionally, four "high quality" genomes were not found in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation and KEGG pathway analysis of the "high-quality" genomes identified seven core genes (antB, dnaB, DNMT1, DUT, xlyAB, xtmB and xtmA) associated with metabolism and fundamental viral processes. Moreover, genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also detected. Host prediction analysis suggest bacterial hosts for approximately 40% of the genomes. Overall, this study reports the discovery of novel viral genomes and provides a comprehensive genome profiling of human gut viruses in a subpopulation from India. These findings serve as a foundation for future biological investigations to elucidate the role of these viruses in host physiology.},
}

Humans
*Genome, Viral
*Metagenome
Feces/virology
*Virome
Metagenomics
*Gastrointestinal Tract/virology
*Viruses/genetics/classification/isolation & purification
Gastrointestinal Microbiome
Phylogeny

@article {pmid40711892,
year = {2025},
author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium, and , },
title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002111},
pmid = {40711892},
issn = {1465-2099},
mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; },
abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.},
}

*Viruses/classification/genetics
*Bacteria/virology
Phylogeny
*Classification/methods

@article {pmid40707990,
year = {2025},
author = {Drevland, OM and de Muinck, EJ and Trosvik, P and Hammerstad, M and Kvitne, KE and Midtvedt, K and Åsberg, A and Robertsen, I},
title = {Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {169},
pmid = {40707990},
issn = {2049-2618},
support = {315792//Norges Forskningsråd/ ; 315792//Norges Forskningsråd/ ; },
mesh = {*Mycophenolic Acid/pharmacokinetics/analogs & derivatives/metabolism ; *Kidney Transplantation ; Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Immunosuppressive Agents/pharmacokinetics/therapeutic use ; Middle Aged ; Feces/microbiology ; Adult ; Transplant Recipients ; Glucuronidase/metabolism/genetics ; Glucuronides/metabolism ; Metagenomics/methods ; *Enterohepatic Circulation ; },
abstract = {BACKGROUND: The pivotal role of microbes in drug metabolism is increasingly recognized, as variation in the gut microbiome composition between individuals has been shown to impact systemic drug exposure, efficacy and toxicity. Mycophenolate mofetil (MMF) is a cornerstone in immunosuppressive therapy following solid organ transplantation. However, dosing and tolerance are challenged by significant pharmacokinetic variability among patients, largely due to variable degrees of enterohepatic recirculation of mycophenolic acid (MPA), the active moiety of MMF. It is hypothesized that the variability in MPA recirculation is driven by gut microbiome-derived β-glucuronidase (β-GUS) mediated cleavage of MPA-glucuronide (MPAG) excreted in the bile. Here, we investigated the bidirectional interaction between MPA and the gut microbiome in kidney transplant recipients, using a combination of in vivo and in vitro data.

RESULTS: We compared the fecal microbiomes of kidney transplant recipients (n = 21) both pre- and post-transplantation to healthy individuals (n = 15) using shotgun metagenomic sequencing. We also determined the individual microbiome-derived reactivation rate of MPAG to MPA and show a strong positive correlation between this reactivation rate and the degree of MPA enterohepatic recirculation in vivo. Through metagenomic analysis, the reactivation rate of MPA was linked to specific gut microbial species. In particular, specific β-GUS gene variants associated with Faecalibacterium prausnitzii showed a strong impact on the conversion of MPAG to MPA. Furthermore, our study confirmed a significant shift in microbial composition post-transplantation and revealed notable fluctuations in species such as F. prausnitzii and Akkermansia muciniphila across different time points after transplantation. Lastly, we provide evidence that the microbiome-derived reactivation rate of MPA is linked to specific beta-glucuronidase alleles.

CONCLUSIONS: We highlight for the first time that the ex vivo determined reactivation rate of MPA explains the variation of enterohepatic recirculation, emphasizing the important role of F. prausnitzii in this process. More broadly, our findings suggest that the gut microbiome significantly influences the degree of enterohepatic recirculation of MPA, providing valuable insights that could be relevant for optimizing individualized immunosuppressive drug dosing in transplant patients. Video Abstract.},
}

*Mycophenolic Acid/pharmacokinetics/analogs & derivatives/metabolism
*Kidney Transplantation
Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
*Immunosuppressive Agents/pharmacokinetics/therapeutic use
Middle Aged
Feces/microbiology
Adult
Transplant Recipients
Glucuronidase/metabolism/genetics
Glucuronides/metabolism
Metagenomics/methods
*Enterohepatic Circulation

@article {pmid40707831,
year = {2025},
author = {Sereika, M and Mussig, AJ and Jiang, C and Knudsen, KS and Jensen, TBN and Petriglieri, F and Yang, Y and Jørgensen, VR and Delogu, F and Sørensen, EA and Nielsen, PH and Singleton, CM and Hugenholtz, P and Albertsen, M},
title = {Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.},
journal = {Nature microbiology},
volume = {10},
number = {8},
pages = {2018-2030},
pmid = {40707831},
issn = {2058-5276},
support = {130690//Villum Fonden (Villum Foundation)/ ; 50093//Villum Fonden (Villum Foundation)/ ; },
mesh = {*Soil Microbiology ; Phylogeny ; Metagenomics/methods ; *Genome, Bacterial ; *Bacteria/genetics/classification/isolation & purification ; Geologic Sediments/microbiology ; *Biodiversity ; Ecosystem ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Nanopore Sequencing ; Sequence Analysis, DNA/methods ; },
abstract = {The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these environments. Here we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected during the Microflora Danica project, yielding genomes of 15,314 previously undescribed microbial species, recovered using our custom mmlong2 workflow. The recovered microbial genomes span 1,086 previously uncharacterized genera and expand the phylogenetic diversity of the prokaryotic tree of life by 8%. The long-read assemblies also enabled the recovery of thousands of complete ribosomal RNA operons, biosynthetic gene clusters and CRISPR-Cas systems. Furthermore, the incorporation of the recovered genomes into public genomic databases substantially improved species-level classification rates for soil and sediment metagenomic datasets. These findings demonstrate that long-read sequencing allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain an untapped source of biodiversity.},
}

*Soil Microbiology
Phylogeny
Metagenomics/methods
*Genome, Bacterial
*Bacteria/genetics/classification/isolation & purification
Geologic Sediments/microbiology
*Biodiversity
Ecosystem
High-Throughput Nucleotide Sequencing/methods
Metagenome
Nanopore Sequencing
Sequence Analysis, DNA/methods

@article {pmid40707722,
year = {2025},
author = {Mangnier, L and Bodein, A and Mariaz, M and Mathieu, A and Scott-Boyer, MP and Vashist, N and Bramble, MS and Droit, A},
title = {A systematic benchmark of integrative strategies for microbiome-metabolome data.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1100},
pmid = {40707722},
issn = {2399-3642},
support = {K01 TW011772/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; *Metabolomics/methods ; *Metabolome ; *Gastrointestinal Microbiome ; Benchmarking ; *Metagenomics/methods ; *Microbiota ; Computational Biology/methods ; },
abstract = {The rapid advancement of high-throughput sequencing technologies has enabled the integration of various omic layers into computational frameworks. Among these, metagenomics and metabolomics are increasingly studied for their roles in complex diseases. However, no standard currently exists for jointly integrating microbiome and metabolome datasets within statistical models. We benchmarked nineteen integrative methods to disentangle the relationships between microorganisms and metabolites. These methods address key research goals, including global associations, data summarization, individual associations, and feature selection. Through realistic simulations, we identified the best-performing methods and validated them on real gut microbiome datasets, revealing complementary biological processes across the two omic layers. Practical guidelines are provided for specific scientific questions and data types. This work establishes a foundation for research standards in metagenomics-metabolomics integration and supports future methodological developments, while also providing guidance for designing optimal analytical strategies tailored to specific integration questions.},
}

Humans
*Metabolomics/methods
*Metabolome
*Gastrointestinal Microbiome
Benchmarking
*Metagenomics/methods
*Microbiota
Computational Biology/methods

@article {pmid40707492,
year = {2025},
author = {Villette, R and Novikova, PV and Laczny, CC and Mollenhauer, B and May, P and Wilmes, P},
title = {Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {142},
pmid = {40707492},
issn = {2055-5008},
support = {863664//HORIZON EUROPE European Research Council/ ; 863664//HORIZON EUROPE European Research Council/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Gene Regulatory Networks ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Aged ; Middle Aged ; },
abstract = {Gut microbiome alterations are linked to various diseases, including neurodegeneration, but their ecological and functional impacts remain unclear. Using integrated multi-omics (metagenomics and metatranscriptomics), we analyse microbiome gene co-expression networks in Parkinson's disease (PD) and healthy controls (HC). We observe a significant depletion of hub genes in PD, including genes involved in secondary bile acid biosynthesis, bacterial microcompartments (BMCs), polysaccharides transport and flagellar assembly (FA). Blautia, Roseburia, Faecalibacterium and Anaerobutyricum genera are the main contributors to these functions, showing significantly lower expression in PD. Additionally, we identify a strong correlation between BMC and FA expression, and an apparent dysregulation in cross-feeding between commensals in PD. Finally, PD also exhibits reduced gene expression diversity compared to HC, whereby higher gene expression correlates with greater diversity. We identify disruptions in gut metabolic functions, at both taxonomic and functional level, and microbiome-wide ecological features, highlighting targets for future gut microbiome restoration efforts.},
}

*Parkinson Disease/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/classification/genetics/isolation & purification/metabolism
*Gene Regulatory Networks
Metagenomics
Gene Expression Profiling
Male
Female
Aged
Middle Aged